data_9NAO # _entry.id 9NAO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.403 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 9NAO pdb_00009nao 10.2210/pdb9nao/pdb WWPDB D_1000292914 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2025-03-26 _pdbx_audit_revision_history.part_number ? # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9NAO _pdbx_database_status.recvd_initial_deposition_date 2025-02-12 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible N # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type PDB 'Same protein in apo-form' 9NAG unspecified PDB 'Same protein complexed with a different ligand' 9N9D unspecified PDB 'Same protein complexed with a different ligand' 9NAE unspecified # _pdbx_contact_author.id 2 _pdbx_contact_author.email jrodriguez@mbi.ucla.edu _pdbx_contact_author.name_first Jose _pdbx_contact_author.name_last Rodriguez _pdbx_contact_author.name_mi A _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-0248-4964 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Vlahakis, N.W.' 1 ? 'Rodriguez, J.A.' 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Biorxiv _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2692-8205 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Combining MicroED and native mass spectrometry for structural discovery of enzyme-biosynthetic inhibitor complexes.' _citation.year 2025 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1101/2025.02.20.638743 _citation.pdbx_database_id_PubMed 40060639 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Vlahakis, N.W.' 1 0000-0002-5092-0265 primary 'Flowers, C.W.' 2 ? primary 'Liu, M.' 3 ? primary 'Agdanowski, M.' 4 ? primary 'Johnson, S.' 5 ? primary 'Summers, J.A.' 6 ? primary 'Keyser, C.' 7 ? primary 'Russell, P.' 8 ? primary 'Rose, S.' 9 ? primary 'Orlans, J.' 10 ? primary 'Adhami, N.' 11 ? primary 'Chen, Y.' 12 ? primary 'Sawaya, M.R.' 13 ? primary 'Basu, S.' 14 ? primary 'de Sanctis, D.' 15 ? primary 'Wakatsuki, S.' 16 ? primary 'Nelson, H.M.' 17 ? primary 'Loo, J.A.' 18 ? primary 'Tang, Y.' 19 ? primary 'Rodriguez, J.A.' 20 0000-0002-0248-4964 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer nat Papain 23452.301 1 3.4.22.2 ? ? ? 2 non-polymer nat '(3S)-4-({(1S)-2-[(8-aminooctyl)amino]-1-cyclobutyl-2-oxoethyl}amino)-3-hydroxy-4-oxobutanoic acid' 371.472 1 ? ? ? ? 3 water nat water 18.015 9 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Papaya proteinase I,PPI' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHA VAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN ; _entity_poly.pdbx_seq_one_letter_code_can ;IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHA VAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '(3S)-4-({(1S)-2-[(8-aminooctyl)amino]-1-cyclobutyl-2-oxoethyl}amino)-3-hydroxy-4-oxobutanoic acid' A1AXI 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ILE n 1 2 PRO n 1 3 GLU n 1 4 TYR n 1 5 VAL n 1 6 ASP n 1 7 TRP n 1 8 ARG n 1 9 GLN n 1 10 LYS n 1 11 GLY n 1 12 ALA n 1 13 VAL n 1 14 THR n 1 15 PRO n 1 16 VAL n 1 17 LYS n 1 18 ASN n 1 19 GLN n 1 20 GLY n 1 21 SER n 1 22 CYS n 1 23 GLY n 1 24 SER n 1 25 CYS n 1 26 TRP n 1 27 ALA n 1 28 PHE n 1 29 SER n 1 30 ALA n 1 31 VAL n 1 32 VAL n 1 33 THR n 1 34 ILE n 1 35 GLU n 1 36 GLY n 1 37 ILE n 1 38 ILE n 1 39 LYS n 1 40 ILE n 1 41 ARG n 1 42 THR n 1 43 GLY n 1 44 ASN n 1 45 LEU n 1 46 ASN n 1 47 GLU n 1 48 TYR n 1 49 SER n 1 50 GLU n 1 51 GLN n 1 52 GLU n 1 53 LEU n 1 54 LEU n 1 55 ASP n 1 56 CYS n 1 57 ASP n 1 58 ARG n 1 59 ARG n 1 60 SER n 1 61 TYR n 1 62 GLY n 1 63 CYS n 1 64 ASN n 1 65 GLY n 1 66 GLY n 1 67 TYR n 1 68 PRO n 1 69 TRP n 1 70 SER n 1 71 ALA n 1 72 LEU n 1 73 GLN n 1 74 LEU n 1 75 VAL n 1 76 ALA n 1 77 GLN n 1 78 TYR n 1 79 GLY n 1 80 ILE n 1 81 HIS n 1 82 TYR n 1 83 ARG n 1 84 ASN n 1 85 THR n 1 86 TYR n 1 87 PRO n 1 88 TYR n 1 89 GLU n 1 90 GLY n 1 91 VAL n 1 92 GLN n 1 93 ARG n 1 94 TYR n 1 95 CYS n 1 96 ARG n 1 97 SER n 1 98 ARG n 1 99 GLU n 1 100 LYS n 1 101 GLY n 1 102 PRO n 1 103 TYR n 1 104 ALA n 1 105 ALA n 1 106 LYS n 1 107 THR n 1 108 ASP n 1 109 GLY n 1 110 VAL n 1 111 ARG n 1 112 GLN n 1 113 VAL n 1 114 GLN n 1 115 PRO n 1 116 TYR n 1 117 ASN n 1 118 GLU n 1 119 GLY n 1 120 ALA n 1 121 LEU n 1 122 LEU n 1 123 TYR n 1 124 SER n 1 125 ILE n 1 126 ALA n 1 127 ASN n 1 128 GLN n 1 129 PRO n 1 130 VAL n 1 131 SER n 1 132 VAL n 1 133 VAL n 1 134 LEU n 1 135 GLU n 1 136 ALA n 1 137 ALA n 1 138 GLY n 1 139 LYS n 1 140 ASP n 1 141 PHE n 1 142 GLN n 1 143 LEU n 1 144 TYR n 1 145 ARG n 1 146 GLY n 1 147 GLY n 1 148 ILE n 1 149 PHE n 1 150 VAL n 1 151 GLY n 1 152 PRO n 1 153 CYS n 1 154 GLY n 1 155 ASN n 1 156 LYS n 1 157 VAL n 1 158 ASP n 1 159 HIS n 1 160 ALA n 1 161 VAL n 1 162 ALA n 1 163 ALA n 1 164 VAL n 1 165 GLY n 1 166 TYR n 1 167 GLY n 1 168 PRO n 1 169 ASN n 1 170 TYR n 1 171 ILE n 1 172 LEU n 1 173 ILE n 1 174 LYS n 1 175 ASN n 1 176 SER n 1 177 TRP n 1 178 GLY n 1 179 THR n 1 180 GLY n 1 181 TRP n 1 182 GLY n 1 183 GLU n 1 184 ASN n 1 185 GLY n 1 186 TYR n 1 187 ILE n 1 188 ARG n 1 189 ILE n 1 190 LYS n 1 191 ARG n 1 192 GLY n 1 193 THR n 1 194 GLY n 1 195 ASN n 1 196 SER n 1 197 TYR n 1 198 GLY n 1 199 VAL n 1 200 CYS n 1 201 GLY n 1 202 LEU n 1 203 TYR n 1 204 THR n 1 205 SER n 1 206 SER n 1 207 PHE n 1 208 TYR n 1 209 PRO n 1 210 VAL n 1 211 LYS n 1 212 ASN n # _entity_src_nat.entity_id 1 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num 1 _entity_src_nat.pdbx_end_seq_num 212 _entity_src_nat.common_name papaya _entity_src_nat.pdbx_organism_scientific 'Carica papaya' _entity_src_nat.pdbx_ncbi_taxonomy_id 3649 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain ? _entity_src_nat.tissue ? _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line ? _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location ? _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A1AXI non-polymer . '(3S)-4-({(1S)-2-[(8-aminooctyl)amino]-1-cyclobutyl-2-oxoethyl}amino)-3-hydroxy-4-oxobutanoic acid' ? 'C18 H33 N3 O5' 371.472 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 ILE 1 1 1 ILE ILE A . n A 1 2 PRO 2 2 2 PRO PRO A . n A 1 3 GLU 3 3 3 GLU GLU A . n A 1 4 TYR 4 4 4 TYR TYR A . n A 1 5 VAL 5 5 5 VAL VAL A . n A 1 6 ASP 6 6 6 ASP ASP A . n A 1 7 TRP 7 7 7 TRP TRP A . n A 1 8 ARG 8 8 8 ARG ARG A . n A 1 9 GLN 9 9 9 GLN GLN A . n A 1 10 LYS 10 10 10 LYS LYS A . n A 1 11 GLY 11 11 11 GLY GLY A . n A 1 12 ALA 12 12 12 ALA ALA A . n A 1 13 VAL 13 13 13 VAL VAL A . n A 1 14 THR 14 14 14 THR THR A . n A 1 15 PRO 15 15 15 PRO PRO A . n A 1 16 VAL 16 16 16 VAL VAL A . n A 1 17 LYS 17 17 17 LYS LYS A . n A 1 18 ASN 18 18 18 ASN ASN A . n A 1 19 GLN 19 19 19 GLN GLN A . n A 1 20 GLY 20 20 20 GLY GLY A . n A 1 21 SER 21 21 21 SER SER A . n A 1 22 CYS 22 22 22 CYS CYS A . n A 1 23 GLY 23 23 23 GLY GLY A . n A 1 24 SER 24 24 24 SER SER A . n A 1 25 CYS 25 25 25 CYS CYS A . n A 1 26 TRP 26 26 26 TRP TRP A . n A 1 27 ALA 27 27 27 ALA ALA A . n A 1 28 PHE 28 28 28 PHE PHE A . n A 1 29 SER 29 29 29 SER SER A . n A 1 30 ALA 30 30 30 ALA ALA A . n A 1 31 VAL 31 31 31 VAL VAL A . n A 1 32 VAL 32 32 32 VAL VAL A . n A 1 33 THR 33 33 33 THR THR A . n A 1 34 ILE 34 34 34 ILE ILE A . n A 1 35 GLU 35 35 35 GLU GLU A . n A 1 36 GLY 36 36 36 GLY GLY A . n A 1 37 ILE 37 37 37 ILE ILE A . n A 1 38 ILE 38 38 38 ILE ILE A . n A 1 39 LYS 39 39 39 LYS LYS A . n A 1 40 ILE 40 40 40 ILE ILE A . n A 1 41 ARG 41 41 41 ARG ARG A . n A 1 42 THR 42 42 42 THR THR A . n A 1 43 GLY 43 43 43 GLY GLY A . n A 1 44 ASN 44 44 44 ASN ASN A . n A 1 45 LEU 45 45 45 LEU LEU A . n A 1 46 ASN 46 46 46 ASN ASN A . n A 1 47 GLU 47 47 47 GLU GLU A . n A 1 48 TYR 48 48 48 TYR TYR A . n A 1 49 SER 49 49 49 SER SER A . n A 1 50 GLU 50 50 50 GLU GLU A . n A 1 51 GLN 51 51 51 GLN GLN A . n A 1 52 GLU 52 52 52 GLU GLU A . n A 1 53 LEU 53 53 53 LEU LEU A . n A 1 54 LEU 54 54 54 LEU LEU A . n A 1 55 ASP 55 55 55 ASP ASP A . n A 1 56 CYS 56 56 56 CYS CYS A . n A 1 57 ASP 57 57 57 ASP ASP A . n A 1 58 ARG 58 58 58 ARG ARG A . n A 1 59 ARG 59 59 59 ARG ARG A . n A 1 60 SER 60 60 60 SER SER A . n A 1 61 TYR 61 61 61 TYR TYR A . n A 1 62 GLY 62 62 62 GLY GLY A . n A 1 63 CYS 63 63 63 CYS CYS A . n A 1 64 ASN 64 64 64 ASN ASN A . n A 1 65 GLY 65 65 65 GLY GLY A . n A 1 66 GLY 66 66 66 GLY GLY A . n A 1 67 TYR 67 67 67 TYR TYR A . n A 1 68 PRO 68 68 68 PRO PRO A . n A 1 69 TRP 69 69 69 TRP TRP A . n A 1 70 SER 70 70 70 SER SER A . n A 1 71 ALA 71 71 71 ALA ALA A . n A 1 72 LEU 72 72 72 LEU LEU A . n A 1 73 GLN 73 73 73 GLN GLN A . n A 1 74 LEU 74 74 74 LEU LEU A . n A 1 75 VAL 75 75 75 VAL VAL A . n A 1 76 ALA 76 76 76 ALA ALA A . n A 1 77 GLN 77 77 77 GLN GLN A . n A 1 78 TYR 78 78 78 TYR TYR A . n A 1 79 GLY 79 79 79 GLY GLY A . n A 1 80 ILE 80 80 80 ILE ILE A . n A 1 81 HIS 81 81 81 HIS HIS A . n A 1 82 TYR 82 82 82 TYR TYR A . n A 1 83 ARG 83 83 83 ARG ARG A . n A 1 84 ASN 84 84 84 ASN ASN A . n A 1 85 THR 85 85 85 THR THR A . n A 1 86 TYR 86 86 86 TYR TYR A . n A 1 87 PRO 87 87 87 PRO PRO A . n A 1 88 TYR 88 88 88 TYR TYR A . n A 1 89 GLU 89 89 89 GLU GLU A . n A 1 90 GLY 90 90 90 GLY GLY A . n A 1 91 VAL 91 91 91 VAL VAL A . n A 1 92 GLN 92 92 92 GLN GLN A . n A 1 93 ARG 93 93 93 ARG ARG A . n A 1 94 TYR 94 94 94 TYR TYR A . n A 1 95 CYS 95 95 95 CYS CYS A . n A 1 96 ARG 96 96 96 ARG ARG A . n A 1 97 SER 97 97 97 SER SER A . n A 1 98 ARG 98 98 98 ARG ARG A . n A 1 99 GLU 99 99 99 GLU GLU A . n A 1 100 LYS 100 100 100 LYS LYS A . n A 1 101 GLY 101 101 101 GLY GLY A . n A 1 102 PRO 102 102 102 PRO PRO A . n A 1 103 TYR 103 103 103 TYR TYR A . n A 1 104 ALA 104 104 104 ALA ALA A . n A 1 105 ALA 105 105 105 ALA ALA A . n A 1 106 LYS 106 106 106 LYS LYS A . n A 1 107 THR 107 107 107 THR THR A . n A 1 108 ASP 108 108 108 ASP ASP A . n A 1 109 GLY 109 109 109 GLY GLY A . n A 1 110 VAL 110 110 110 VAL VAL A . n A 1 111 ARG 111 111 111 ARG ARG A . n A 1 112 GLN 112 112 112 GLN GLN A . n A 1 113 VAL 113 113 113 VAL VAL A . n A 1 114 GLN 114 114 114 GLN GLN A . n A 1 115 PRO 115 115 115 PRO PRO A . n A 1 116 TYR 116 116 116 TYR TYR A . n A 1 117 ASN 117 117 117 ASN ASN A . n A 1 118 GLU 118 118 118 GLU GLU A . n A 1 119 GLY 119 119 119 GLY GLY A . n A 1 120 ALA 120 120 120 ALA ALA A . n A 1 121 LEU 121 121 121 LEU LEU A . n A 1 122 LEU 122 122 122 LEU LEU A . n A 1 123 TYR 123 123 123 TYR TYR A . n A 1 124 SER 124 124 124 SER SER A . n A 1 125 ILE 125 125 125 ILE ILE A . n A 1 126 ALA 126 126 126 ALA ALA A . n A 1 127 ASN 127 127 127 ASN ASN A . n A 1 128 GLN 128 128 128 GLN GLN A . n A 1 129 PRO 129 129 129 PRO PRO A . n A 1 130 VAL 130 130 130 VAL VAL A . n A 1 131 SER 131 131 131 SER SER A . n A 1 132 VAL 132 132 132 VAL VAL A . n A 1 133 VAL 133 133 133 VAL VAL A . n A 1 134 LEU 134 134 134 LEU LEU A . n A 1 135 GLU 135 135 135 GLU GLU A . n A 1 136 ALA 136 136 136 ALA ALA A . n A 1 137 ALA 137 137 137 ALA ALA A . n A 1 138 GLY 138 138 138 GLY GLY A . n A 1 139 LYS 139 139 139 LYS LYS A . n A 1 140 ASP 140 140 140 ASP ASP A . n A 1 141 PHE 141 141 141 PHE PHE A . n A 1 142 GLN 142 142 142 GLN GLN A . n A 1 143 LEU 143 143 143 LEU LEU A . n A 1 144 TYR 144 144 144 TYR TYR A . n A 1 145 ARG 145 145 145 ARG ARG A . n A 1 146 GLY 146 146 146 GLY GLY A . n A 1 147 GLY 147 147 147 GLY GLY A . n A 1 148 ILE 148 148 148 ILE ILE A . n A 1 149 PHE 149 149 149 PHE PHE A . n A 1 150 VAL 150 150 150 VAL VAL A . n A 1 151 GLY 151 151 151 GLY GLY A . n A 1 152 PRO 152 152 152 PRO PRO A . n A 1 153 CYS 153 153 153 CYS CYS A . n A 1 154 GLY 154 154 154 GLY GLY A . n A 1 155 ASN 155 155 155 ASN ASN A . n A 1 156 LYS 156 156 156 LYS LYS A . n A 1 157 VAL 157 157 157 VAL VAL A . n A 1 158 ASP 158 158 158 ASP ASP A . n A 1 159 HIS 159 159 159 HIS HIS A . n A 1 160 ALA 160 160 160 ALA ALA A . n A 1 161 VAL 161 161 161 VAL VAL A . n A 1 162 ALA 162 162 162 ALA ALA A . n A 1 163 ALA 163 163 163 ALA ALA A . n A 1 164 VAL 164 164 164 VAL VAL A . n A 1 165 GLY 165 165 165 GLY GLY A . n A 1 166 TYR 166 166 166 TYR TYR A . n A 1 167 GLY 167 167 167 GLY GLY A . n A 1 168 PRO 168 168 168 PRO PRO A . n A 1 169 ASN 169 169 169 ASN ASN A . n A 1 170 TYR 170 170 170 TYR TYR A . n A 1 171 ILE 171 171 171 ILE ILE A . n A 1 172 LEU 172 172 172 LEU LEU A . n A 1 173 ILE 173 173 173 ILE ILE A . n A 1 174 LYS 174 174 174 LYS LYS A . n A 1 175 ASN 175 175 175 ASN ASN A . n A 1 176 SER 176 176 176 SER SER A . n A 1 177 TRP 177 177 177 TRP TRP A . n A 1 178 GLY 178 178 178 GLY GLY A . n A 1 179 THR 179 179 179 THR THR A . n A 1 180 GLY 180 180 180 GLY GLY A . n A 1 181 TRP 181 181 181 TRP TRP A . n A 1 182 GLY 182 182 182 GLY GLY A . n A 1 183 GLU 183 183 183 GLU GLU A . n A 1 184 ASN 184 184 184 ASN ASN A . n A 1 185 GLY 185 185 185 GLY GLY A . n A 1 186 TYR 186 186 186 TYR TYR A . n A 1 187 ILE 187 187 187 ILE ILE A . n A 1 188 ARG 188 188 188 ARG ARG A . n A 1 189 ILE 189 189 189 ILE ILE A . n A 1 190 LYS 190 190 190 LYS LYS A . n A 1 191 ARG 191 191 191 ARG ARG A . n A 1 192 GLY 192 192 192 GLY GLY A . n A 1 193 THR 193 193 193 THR THR A . n A 1 194 GLY 194 194 194 GLY GLY A . n A 1 195 ASN 195 195 195 ASN ASN A . n A 1 196 SER 196 196 196 SER SER A . n A 1 197 TYR 197 197 197 TYR TYR A . n A 1 198 GLY 198 198 198 GLY GLY A . n A 1 199 VAL 199 199 199 VAL VAL A . n A 1 200 CYS 200 200 200 CYS CYS A . n A 1 201 GLY 201 201 201 GLY GLY A . n A 1 202 LEU 202 202 202 LEU LEU A . n A 1 203 TYR 203 203 203 TYR TYR A . n A 1 204 THR 204 204 204 THR THR A . n A 1 205 SER 205 205 205 SER SER A . n A 1 206 SER 206 206 206 SER SER A . n A 1 207 PHE 207 207 207 PHE PHE A . n A 1 208 TYR 208 208 208 TYR TYR A . n A 1 209 PRO 209 209 209 PRO PRO A . n A 1 210 VAL 210 210 210 VAL VAL A . n A 1 211 LYS 211 211 211 LYS LYS A . n A 1 212 ASN 212 212 212 ASN ASN A . n # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id A1AXI _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id A1AXI _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 A1AXI 1 301 301 A1AXI A65 A . C 3 HOH 1 401 7 HOH HOH A . C 3 HOH 2 402 3 HOH HOH A . C 3 HOH 3 403 1 HOH HOH A . C 3 HOH 4 404 4 HOH HOH A . C 3 HOH 5 405 11 HOH HOH A . C 3 HOH 6 406 8 HOH HOH A . C 3 HOH 7 407 5 HOH HOH A . C 3 HOH 8 408 6 HOH HOH A . C 3 HOH 9 409 9 HOH HOH A . # loop_ _software.classification _software.name _software.version _software.citation_id _software.pdbx_ordinal refinement PHENIX 1.20.1_4487 ? 1 'data scaling' XSCALE . ? 2 'data reduction' XDS . ? 3 phasing PHASER . ? 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 9NAO _cell.details ? _cell.formula_units_Z ? _cell.length_a 42.310 _cell.length_a_esd ? _cell.length_b 48.320 _cell.length_b_esd ? _cell.length_c 100.480 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 4 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9NAO _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 9NAO _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON CRYSTALLOGRAPHY' _exptl.method_details ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 9NAO _refine.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.50 _refine.ls_d_res_low 50.24 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 6605 _refine.ls_number_reflns_R_free 661 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 87.30 _refine.ls_percent_reflns_R_free 10.01 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2367 _refine.ls_R_factor_R_free 0.2646 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2335 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.correlation_coeff_I_to_Fcsqd_work ? _refine.correlation_coeff_I_to_Fcsqd_free ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.34 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.10 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 26.64 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.27 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'ELECTRON CRYSTALLOGRAPHY' ? 0.007 ? 1797 ? f_bond_d ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 1.044 ? 2449 ? f_angle_d ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 7.998 ? 278 ? f_dihedral_angle_d ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.068 ? 242 ? f_chiral_restr ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.008 ? 323 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.correlation_coeff_Fo_to_Fc _refine_ls_shell.correlation_coeff_Fo_to_Fc_free _refine_ls_shell.correlation_coeff_I_to_Fcsqd_work _refine_ls_shell.correlation_coeff_I_to_Fcsqd_free _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'ELECTRON CRYSTALLOGRAPHY' 2.50 2.69 . . 130 1178 88.00 . . . . 0.3197 . . . . . . . . . . . . . . . 0.3455 'ELECTRON CRYSTALLOGRAPHY' 2.69 2.96 . . 132 1181 89.00 . . . . 0.2988 . . . . . . . . . . . . . . . 0.3387 'ELECTRON CRYSTALLOGRAPHY' 2.96 3.39 . . 134 1199 89.00 . . . . 0.2563 . . . . . . . . . . . . . . . 0.2812 'ELECTRON CRYSTALLOGRAPHY' 3.39 4.27 . . 133 1200 88.00 . . . . 0.2033 . . . . . . . . . . . . . . . 0.2269 'ELECTRON CRYSTALLOGRAPHY' 4.27 50.24 . . 132 1186 83.00 . . . . 0.1946 . . . . . . . . . . . . . . . 0.2338 # _struct.entry_id 9NAO _struct.title 'MicroED structure of papain complexed with natural product E64-A65' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 9NAO _struct_keywords.text 'Inhibitor, Complex, Protease, MicroED, HYDROLASE' _struct_keywords.pdbx_keywords HYDROLASE # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code PAPA1_CARPA _struct_ref.pdbx_db_accession P00784 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHA VAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN ; _struct_ref.pdbx_align_begin 134 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 9NAO _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 212 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P00784 _struct_ref_seq.db_align_beg 134 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 345 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 212 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 SER A 24 ? GLY A 43 ? SER A 24 GLY A 43 1 ? 20 HELX_P HELX_P2 AA2 SER A 49 ? ASP A 57 ? SER A 49 ASP A 57 1 ? 9 HELX_P HELX_P3 AA3 TYR A 61 ? GLY A 65 ? TYR A 61 GLY A 65 5 ? 5 HELX_P HELX_P4 AA4 TYR A 67 ? TYR A 78 ? TYR A 67 TYR A 78 1 ? 12 HELX_P HELX_P5 AA5 ARG A 96 ? GLY A 101 ? ARG A 96 GLY A 101 5 ? 6 HELX_P HELX_P6 AA6 ASN A 117 ? GLN A 128 ? ASN A 117 GLN A 128 1 ? 12 HELX_P HELX_P7 AA7 GLY A 138 ? LEU A 143 ? GLY A 138 LEU A 143 1 ? 6 HELX_P HELX_P8 AA8 GLY A 198 ? LEU A 202 ? GLY A 198 LEU A 202 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 22 SG ? ? ? 1_555 A CYS 63 SG ? ? A CYS 22 A CYS 63 1_555 ? ? ? ? ? ? ? 2.041 ? ? disulf2 disulf ? ? A CYS 56 SG ? ? ? 1_555 A CYS 95 SG ? ? A CYS 56 A CYS 95 1_555 ? ? ? ? ? ? ? 2.039 ? ? disulf3 disulf ? ? A CYS 153 SG ? ? ? 1_555 A CYS 200 SG ? ? A CYS 153 A CYS 200 1_555 ? ? ? ? ? ? ? 2.058 ? ? covale1 covale none ? A CYS 25 SG ? ? ? 1_555 B A1AXI . C2 ? ? A CYS 25 A A1AXI 301 1_555 ? ? ? ? ? ? ? 1.807 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # loop_ _pdbx_modification_feature.ordinal _pdbx_modification_feature.label_comp_id _pdbx_modification_feature.label_asym_id _pdbx_modification_feature.label_seq_id _pdbx_modification_feature.label_alt_id _pdbx_modification_feature.modified_residue_label_comp_id _pdbx_modification_feature.modified_residue_label_asym_id _pdbx_modification_feature.modified_residue_label_seq_id _pdbx_modification_feature.modified_residue_label_alt_id _pdbx_modification_feature.auth_comp_id _pdbx_modification_feature.auth_asym_id _pdbx_modification_feature.auth_seq_id _pdbx_modification_feature.PDB_ins_code _pdbx_modification_feature.symmetry _pdbx_modification_feature.modified_residue_auth_comp_id _pdbx_modification_feature.modified_residue_auth_asym_id _pdbx_modification_feature.modified_residue_auth_seq_id _pdbx_modification_feature.modified_residue_PDB_ins_code _pdbx_modification_feature.modified_residue_symmetry _pdbx_modification_feature.comp_id_linking_atom _pdbx_modification_feature.modified_residue_id_linking_atom _pdbx_modification_feature.modified_residue_id _pdbx_modification_feature.ref_pcm_id _pdbx_modification_feature.ref_comp_id _pdbx_modification_feature.type _pdbx_modification_feature.category 1 A1AXI B . ? CYS A 25 ? A1AXI A 301 ? 1_555 CYS A 25 ? 1_555 C2 SG CYS 1 A1AXI None 'Covalent chemical modification' 2 CYS A 22 ? CYS A 63 ? CYS A 22 ? 1_555 CYS A 63 ? 1_555 SG SG . . . None 'Disulfide bridge' 3 CYS A 56 ? CYS A 95 ? CYS A 56 ? 1_555 CYS A 95 ? 1_555 SG SG . . . None 'Disulfide bridge' 4 CYS A 153 ? CYS A 200 ? CYS A 153 ? 1_555 CYS A 200 ? 1_555 SG SG . . . None 'Disulfide bridge' # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id GLY _struct_mon_prot_cis.label_seq_id 151 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id GLY _struct_mon_prot_cis.auth_seq_id 151 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 152 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 152 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle 2.67 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 3 ? AA2 ? 5 ? AA3 ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel AA2 3 4 ? anti-parallel AA2 4 5 ? parallel AA3 1 2 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 VAL A 5 ? ASP A 6 ? VAL A 5 ASP A 6 AA1 2 HIS A 159 ? GLY A 167 ? HIS A 159 GLY A 167 AA1 3 VAL A 130 ? LEU A 134 ? VAL A 130 LEU A 134 AA2 1 VAL A 5 ? ASP A 6 ? VAL A 5 ASP A 6 AA2 2 HIS A 159 ? GLY A 167 ? HIS A 159 GLY A 167 AA2 3 TYR A 170 ? LYS A 174 ? TYR A 170 LYS A 174 AA2 4 TYR A 186 ? LYS A 190 ? TYR A 186 LYS A 190 AA2 5 ILE A 148 ? PHE A 149 ? ILE A 148 PHE A 149 AA3 1 GLY A 109 ? GLN A 112 ? GLY A 109 GLN A 112 AA3 2 PHE A 207 ? VAL A 210 ? PHE A 207 VAL A 210 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N VAL A 5 ? N VAL A 5 O TYR A 166 ? O TYR A 166 AA1 2 3 O ALA A 163 ? O ALA A 163 N VAL A 130 ? N VAL A 130 AA2 1 2 N VAL A 5 ? N VAL A 5 O TYR A 166 ? O TYR A 166 AA2 2 3 N ALA A 162 ? N ALA A 162 O LYS A 174 ? O LYS A 174 AA2 3 4 N ILE A 173 ? N ILE A 173 O ILE A 187 ? O ILE A 187 AA2 4 5 O ARG A 188 ? O ARG A 188 N PHE A 149 ? N PHE A 149 AA3 1 2 N ARG A 111 ? N ARG A 111 O TYR A 208 ? O TYR A 208 # _pdbx_entry_details.entry_id 9NAO _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.has_protein_modification Y # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 TYR A 78 ? ? -102.60 -69.11 2 1 ARG A 93 ? ? -128.44 -111.54 3 1 ARG A 93 ? ? -128.44 -108.27 4 1 ASN A 155 ? ? -109.47 43.67 5 1 ASP A 158 ? ? -153.54 7.31 6 1 SER A 205 ? ? -160.16 101.27 # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9NAO _em_3d_fitting.method ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_space ? _em_3d_fitting.ref_protocol ? # _em_3d_fitting_list.id 1 _em_3d_fitting_list.3d_fitting_id 1 _em_3d_fitting_list.pdb_entry_id 9PAP _em_3d_fitting_list.pdb_chain_id ? _em_3d_fitting_list.pdb_chain_residue_range ? _em_3d_fitting_list.details ? _em_3d_fitting_list.chain_id ? _em_3d_fitting_list.chain_residue_range ? _em_3d_fitting_list.source_name PDB _em_3d_fitting_list.type 'experimental model' _em_3d_fitting_list.accession_code 9PAP _em_3d_fitting_list.initial_refinement_model_id 1 # _em_3d_reconstruction.entry_id 9NAO _em_3d_reconstruction.id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.details ? _em_3d_reconstruction.resolution 2.5 _em_3d_reconstruction.resolution_method 'DIFFRACTION PATTERN/LAYERLINES' _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.num_particles ? _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type '3D CRYSTAL' # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details ? _em_buffer.pH 7 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source NATURAL _em_entity_assembly.type COMPLEX _em_entity_assembly.name 'Papain-E64-A65 complex' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 9NAO _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'TFS TALOS F200C' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model 'GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER' _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 200 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode DIFFRACTION _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_min 10000 _em_imaging.nominal_defocus_max 10000 _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_defocus_max ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_magnification ? _em_imaging.calibrated_magnification ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.citation_id ? _em_imaging.temperature ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_minimum 100 _em_imaging.recording_temperature_maximum 100 _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter 70 _em_imaging.specimen_id 1 _em_imaging.cryogen ? _em_imaging.objective_aperture ? _em_imaging.microscope_serial_number ? _em_imaging.microscope_version ? # _em_vitrification.entry_id 9NAO _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity ? _em_vitrification.temp ? _em_vitrification.chamber_temperature ? _em_vitrification.instrument ? _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 9NAO _em_experiment.id 1 _em_experiment.reconstruction_method CRYSTALLOGRAPHY _em_experiment.aggregation_state '3D ARRAY' _em_experiment.entity_assembly_id 1 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A1AXI N1 N N N 1 A1AXI N3 N N N 2 A1AXI C4 C N N 3 A1AXI C5 C N S 4 A1AXI C6 C N N 5 A1AXI C7 C N N 6 A1AXI C8 C N N 7 A1AXI C10 C N N 8 A1AXI C13 C N N 9 A1AXI C15 C N N 10 A1AXI C17 C N N 11 A1AXI C1 C N N 12 A1AXI C11 C N N 13 A1AXI C12 C N N 14 A1AXI C14 C N N 15 A1AXI C16 C N N 16 A1AXI C18 C N N 17 A1AXI C2 C N N 18 A1AXI C3 C N S 19 A1AXI C9 C N N 20 A1AXI N2 N N N 21 A1AXI O1 O N N 22 A1AXI O2 O N N 23 A1AXI O3 O N N 24 A1AXI O4 O N N 25 A1AXI O5 O N N 26 A1AXI H1 H N N 27 A1AXI H2 H N N 28 A1AXI H3 H N N 29 A1AXI H5 H N N 30 A1AXI H6 H N N 31 A1AXI H7 H N N 32 A1AXI H8 H N N 33 A1AXI H9 H N N 34 A1AXI H10 H N N 35 A1AXI H11 H N N 36 A1AXI H12 H N N 37 A1AXI H13 H N N 38 A1AXI H14 H N N 39 A1AXI H15 H N N 40 A1AXI H16 H N N 41 A1AXI H17 H N N 42 A1AXI H18 H N N 43 A1AXI H19 H N N 44 A1AXI H20 H N N 45 A1AXI H21 H N N 46 A1AXI H22 H N N 47 A1AXI H23 H N N 48 A1AXI H24 H N N 49 A1AXI H25 H N N 50 A1AXI H26 H N N 51 A1AXI H27 H N N 52 A1AXI H28 H N N 53 A1AXI H29 H N N 54 A1AXI H30 H N N 55 A1AXI H31 H N N 56 A1AXI H32 H N N 57 A1AXI H33 H N N 58 A1AXI H34 H N N 59 ALA N N N N 60 ALA CA C N S 61 ALA C C N N 62 ALA O O N N 63 ALA CB C N N 64 ALA OXT O N N 65 ALA H H N N 66 ALA H2 H N N 67 ALA HA H N N 68 ALA HB1 H N N 69 ALA HB2 H N N 70 ALA HB3 H N N 71 ALA HXT H N N 72 ARG N N N N 73 ARG CA C N S 74 ARG C C N N 75 ARG O O N N 76 ARG CB C N N 77 ARG CG C N N 78 ARG CD C N N 79 ARG NE N N N 80 ARG CZ C N N 81 ARG NH1 N N N 82 ARG NH2 N N N 83 ARG OXT O N N 84 ARG H H N N 85 ARG H2 H N N 86 ARG HA H N N 87 ARG HB2 H N N 88 ARG HB3 H N N 89 ARG HG2 H N N 90 ARG HG3 H N N 91 ARG HD2 H N N 92 ARG HD3 H N N 93 ARG HE H N N 94 ARG HH11 H N N 95 ARG HH12 H N N 96 ARG HH21 H N N 97 ARG HH22 H N N 98 ARG HXT H N N 99 ASN N N N N 100 ASN CA C N S 101 ASN C C N N 102 ASN O O N N 103 ASN CB C N N 104 ASN CG C N N 105 ASN OD1 O N N 106 ASN ND2 N N N 107 ASN OXT O N N 108 ASN H H N N 109 ASN H2 H N N 110 ASN HA H N N 111 ASN HB2 H N N 112 ASN HB3 H N N 113 ASN HD21 H N N 114 ASN HD22 H N N 115 ASN HXT H N N 116 ASP N N N N 117 ASP CA C N S 118 ASP C C N N 119 ASP O O N N 120 ASP CB C N N 121 ASP CG C N N 122 ASP OD1 O N N 123 ASP OD2 O N N 124 ASP OXT O N N 125 ASP H H N N 126 ASP H2 H N N 127 ASP HA H N N 128 ASP HB2 H N N 129 ASP HB3 H N N 130 ASP HD2 H N N 131 ASP HXT H N N 132 CYS N N N N 133 CYS CA C N R 134 CYS C C N N 135 CYS O O N N 136 CYS CB C N N 137 CYS SG S N N 138 CYS OXT O N N 139 CYS H H N N 140 CYS H2 H N N 141 CYS HA H N N 142 CYS HB2 H N N 143 CYS HB3 H N N 144 CYS HG H N N 145 CYS HXT H N N 146 GLN N N N N 147 GLN CA C N S 148 GLN C C N N 149 GLN O O N N 150 GLN CB C N N 151 GLN CG C N N 152 GLN CD C N N 153 GLN OE1 O N N 154 GLN NE2 N N N 155 GLN OXT O N N 156 GLN H H N N 157 GLN H2 H N N 158 GLN HA H N N 159 GLN HB2 H N N 160 GLN HB3 H N N 161 GLN HG2 H N N 162 GLN HG3 H N N 163 GLN HE21 H N N 164 GLN HE22 H N N 165 GLN HXT H N N 166 GLU N N N N 167 GLU CA C N S 168 GLU C C N N 169 GLU O O N N 170 GLU CB C N N 171 GLU CG C N N 172 GLU CD C N N 173 GLU OE1 O N N 174 GLU OE2 O N N 175 GLU OXT O N N 176 GLU H H N N 177 GLU H2 H N N 178 GLU HA H N N 179 GLU HB2 H N N 180 GLU HB3 H N N 181 GLU HG2 H N N 182 GLU HG3 H N N 183 GLU HE2 H N N 184 GLU HXT H N N 185 GLY N N N N 186 GLY CA C N N 187 GLY C C N N 188 GLY O O N N 189 GLY OXT O N N 190 GLY H H N N 191 GLY H2 H N N 192 GLY HA2 H N N 193 GLY HA3 H N N 194 GLY HXT H N N 195 HIS N N N N 196 HIS CA C N S 197 HIS C C N N 198 HIS O O N N 199 HIS CB C N N 200 HIS CG C Y N 201 HIS ND1 N Y N 202 HIS CD2 C Y N 203 HIS CE1 C Y N 204 HIS NE2 N Y N 205 HIS OXT O N N 206 HIS H H N N 207 HIS H2 H N N 208 HIS HA H N N 209 HIS HB2 H N N 210 HIS HB3 H N N 211 HIS HD1 H N N 212 HIS HD2 H N N 213 HIS HE1 H N N 214 HIS HE2 H N N 215 HIS HXT H N N 216 HOH O O N N 217 HOH H1 H N N 218 HOH H2 H N N 219 ILE N N N N 220 ILE CA C N S 221 ILE C C N N 222 ILE O O N N 223 ILE CB C N S 224 ILE CG1 C N N 225 ILE CG2 C N N 226 ILE CD1 C N N 227 ILE OXT O N N 228 ILE H H N N 229 ILE H2 H N N 230 ILE HA H N N 231 ILE HB H N N 232 ILE HG12 H N N 233 ILE HG13 H N N 234 ILE HG21 H N N 235 ILE HG22 H N N 236 ILE HG23 H N N 237 ILE HD11 H N N 238 ILE HD12 H N N 239 ILE HD13 H N N 240 ILE HXT H N N 241 LEU N N N N 242 LEU CA C N S 243 LEU C C N N 244 LEU O O N N 245 LEU CB C N N 246 LEU CG C N N 247 LEU CD1 C N N 248 LEU CD2 C N N 249 LEU OXT O N N 250 LEU H H N N 251 LEU H2 H N N 252 LEU HA H N N 253 LEU HB2 H N N 254 LEU HB3 H N N 255 LEU HG H N N 256 LEU HD11 H N N 257 LEU HD12 H N N 258 LEU HD13 H N N 259 LEU HD21 H N N 260 LEU HD22 H N N 261 LEU HD23 H N N 262 LEU HXT H N N 263 LYS N N N N 264 LYS CA C N S 265 LYS C C N N 266 LYS O O N N 267 LYS CB C N N 268 LYS CG C N N 269 LYS CD C N N 270 LYS CE C N N 271 LYS NZ N N N 272 LYS OXT O N N 273 LYS H H N N 274 LYS H2 H N N 275 LYS HA H N N 276 LYS HB2 H N N 277 LYS HB3 H N N 278 LYS HG2 H N N 279 LYS HG3 H N N 280 LYS HD2 H N N 281 LYS HD3 H N N 282 LYS HE2 H N N 283 LYS HE3 H N N 284 LYS HZ1 H N N 285 LYS HZ2 H N N 286 LYS HZ3 H N N 287 LYS HXT H N N 288 PHE N N N N 289 PHE CA C N S 290 PHE C C N N 291 PHE O O N N 292 PHE CB C N N 293 PHE CG C Y N 294 PHE CD1 C Y N 295 PHE CD2 C Y N 296 PHE CE1 C Y N 297 PHE CE2 C Y N 298 PHE CZ C Y N 299 PHE OXT O N N 300 PHE H H N N 301 PHE H2 H N N 302 PHE HA H N N 303 PHE HB2 H N N 304 PHE HB3 H N N 305 PHE HD1 H N N 306 PHE HD2 H N N 307 PHE HE1 H N N 308 PHE HE2 H N N 309 PHE HZ H N N 310 PHE HXT H N N 311 PRO N N N N 312 PRO CA C N S 313 PRO C C N N 314 PRO O O N N 315 PRO CB C N N 316 PRO CG C N N 317 PRO CD C N N 318 PRO OXT O N N 319 PRO H H N N 320 PRO HA H N N 321 PRO HB2 H N N 322 PRO HB3 H N N 323 PRO HG2 H N N 324 PRO HG3 H N N 325 PRO HD2 H N N 326 PRO HD3 H N N 327 PRO HXT H N N 328 SER N N N N 329 SER CA C N S 330 SER C C N N 331 SER O O N N 332 SER CB C N N 333 SER OG O N N 334 SER OXT O N N 335 SER H H N N 336 SER H2 H N N 337 SER HA H N N 338 SER HB2 H N N 339 SER HB3 H N N 340 SER HG H N N 341 SER HXT H N N 342 THR N N N N 343 THR CA C N S 344 THR C C N N 345 THR O O N N 346 THR CB C N R 347 THR OG1 O N N 348 THR CG2 C N N 349 THR OXT O N N 350 THR H H N N 351 THR H2 H N N 352 THR HA H N N 353 THR HB H N N 354 THR HG1 H N N 355 THR HG21 H N N 356 THR HG22 H N N 357 THR HG23 H N N 358 THR HXT H N N 359 TRP N N N N 360 TRP CA C N S 361 TRP C C N N 362 TRP O O N N 363 TRP CB C N N 364 TRP CG C Y N 365 TRP CD1 C Y N 366 TRP CD2 C Y N 367 TRP NE1 N Y N 368 TRP CE2 C Y N 369 TRP CE3 C Y N 370 TRP CZ2 C Y N 371 TRP CZ3 C Y N 372 TRP CH2 C Y N 373 TRP OXT O N N 374 TRP H H N N 375 TRP H2 H N N 376 TRP HA H N N 377 TRP HB2 H N N 378 TRP HB3 H N N 379 TRP HD1 H N N 380 TRP HE1 H N N 381 TRP HE3 H N N 382 TRP HZ2 H N N 383 TRP HZ3 H N N 384 TRP HH2 H N N 385 TRP HXT H N N 386 TYR N N N N 387 TYR CA C N S 388 TYR C C N N 389 TYR O O N N 390 TYR CB C N N 391 TYR CG C Y N 392 TYR CD1 C Y N 393 TYR CD2 C Y N 394 TYR CE1 C Y N 395 TYR CE2 C Y N 396 TYR CZ C Y N 397 TYR OH O N N 398 TYR OXT O N N 399 TYR H H N N 400 TYR H2 H N N 401 TYR HA H N N 402 TYR HB2 H N N 403 TYR HB3 H N N 404 TYR HD1 H N N 405 TYR HD2 H N N 406 TYR HE1 H N N 407 TYR HE2 H N N 408 TYR HH H N N 409 TYR HXT H N N 410 VAL N N N N 411 VAL CA C N S 412 VAL C C N N 413 VAL O O N N 414 VAL CB C N N 415 VAL CG1 C N N 416 VAL CG2 C N N 417 VAL OXT O N N 418 VAL H H N N 419 VAL H2 H N N 420 VAL HA H N N 421 VAL HB H N N 422 VAL HG11 H N N 423 VAL HG12 H N N 424 VAL HG13 H N N 425 VAL HG21 H N N 426 VAL HG22 H N N 427 VAL HG23 H N N 428 VAL HXT H N N 429 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A1AXI O2 C1 doub N N 1 A1AXI C1 O1 sing N N 2 A1AXI C1 C2 sing N N 3 A1AXI C2 C3 sing N N 4 A1AXI C3 O3 sing N N 5 A1AXI C3 C4 sing N N 6 A1AXI O4 C4 doub N N 7 A1AXI C4 N1 sing N N 8 A1AXI N1 C5 sing N N 9 A1AXI C5 C10 sing N N 10 A1AXI C5 C6 sing N N 11 A1AXI C8 C7 sing N N 12 A1AXI C8 C9 sing N N 13 A1AXI C7 C6 sing N N 14 A1AXI C16 C17 sing N N 15 A1AXI C16 C15 sing N N 16 A1AXI N2 C10 sing N N 17 A1AXI N2 C11 sing N N 18 A1AXI C12 C11 sing N N 19 A1AXI C12 C13 sing N N 20 A1AXI C14 C13 sing N N 21 A1AXI C14 C15 sing N N 22 A1AXI C10 O5 doub N N 23 A1AXI C6 C9 sing N N 24 A1AXI C17 C18 sing N N 25 A1AXI C18 N3 sing N N 26 A1AXI N1 H1 sing N N 27 A1AXI N3 H2 sing N N 28 A1AXI N3 H3 sing N N 29 A1AXI C5 H5 sing N N 30 A1AXI C6 H6 sing N N 31 A1AXI C7 H7 sing N N 32 A1AXI C7 H8 sing N N 33 A1AXI C8 H9 sing N N 34 A1AXI C8 H10 sing N N 35 A1AXI C13 H11 sing N N 36 A1AXI C13 H12 sing N N 37 A1AXI C15 H13 sing N N 38 A1AXI C15 H14 sing N N 39 A1AXI C17 H15 sing N N 40 A1AXI C17 H16 sing N N 41 A1AXI C11 H17 sing N N 42 A1AXI C11 H18 sing N N 43 A1AXI C12 H19 sing N N 44 A1AXI C12 H20 sing N N 45 A1AXI C14 H21 sing N N 46 A1AXI C14 H22 sing N N 47 A1AXI C16 H23 sing N N 48 A1AXI C16 H24 sing N N 49 A1AXI C18 H25 sing N N 50 A1AXI C18 H26 sing N N 51 A1AXI C2 H27 sing N N 52 A1AXI C2 H28 sing N N 53 A1AXI C3 H29 sing N N 54 A1AXI C9 H30 sing N N 55 A1AXI C9 H31 sing N N 56 A1AXI N2 H32 sing N N 57 A1AXI O1 H33 sing N N 58 A1AXI O3 H34 sing N N 59 ALA N CA sing N N 60 ALA N H sing N N 61 ALA N H2 sing N N 62 ALA CA C sing N N 63 ALA CA CB sing N N 64 ALA CA HA sing N N 65 ALA C O doub N N 66 ALA C OXT sing N N 67 ALA CB HB1 sing N N 68 ALA CB HB2 sing N N 69 ALA CB HB3 sing N N 70 ALA OXT HXT sing N N 71 ARG N CA sing N N 72 ARG N H sing N N 73 ARG N H2 sing N N 74 ARG CA C sing N N 75 ARG CA CB sing N N 76 ARG CA HA sing N N 77 ARG C O doub N N 78 ARG C OXT sing N N 79 ARG CB CG sing N N 80 ARG CB HB2 sing N N 81 ARG CB HB3 sing N N 82 ARG CG CD sing N N 83 ARG CG HG2 sing N N 84 ARG CG HG3 sing N N 85 ARG CD NE sing N N 86 ARG CD HD2 sing N N 87 ARG CD HD3 sing N N 88 ARG NE CZ sing N N 89 ARG NE HE sing N N 90 ARG CZ NH1 sing N N 91 ARG CZ NH2 doub N N 92 ARG NH1 HH11 sing N N 93 ARG NH1 HH12 sing N N 94 ARG NH2 HH21 sing N N 95 ARG NH2 HH22 sing N N 96 ARG OXT HXT sing N N 97 ASN N CA sing N N 98 ASN N H sing N N 99 ASN N H2 sing N N 100 ASN CA C sing N N 101 ASN CA CB sing N N 102 ASN CA HA sing N N 103 ASN C O doub N N 104 ASN C OXT sing N N 105 ASN CB CG sing N N 106 ASN CB HB2 sing N N 107 ASN CB HB3 sing N N 108 ASN CG OD1 doub N N 109 ASN CG ND2 sing N N 110 ASN ND2 HD21 sing N N 111 ASN ND2 HD22 sing N N 112 ASN OXT HXT sing N N 113 ASP N CA sing N N 114 ASP N H sing N N 115 ASP N H2 sing N N 116 ASP CA C sing N N 117 ASP CA CB sing N N 118 ASP CA HA sing N N 119 ASP C O doub N N 120 ASP C OXT sing N N 121 ASP CB CG sing N N 122 ASP CB HB2 sing N N 123 ASP CB HB3 sing N N 124 ASP CG OD1 doub N N 125 ASP CG OD2 sing N N 126 ASP OD2 HD2 sing N N 127 ASP OXT HXT sing N N 128 CYS N CA sing N N 129 CYS N H sing N N 130 CYS N H2 sing N N 131 CYS CA C sing N N 132 CYS CA CB sing N N 133 CYS CA HA sing N N 134 CYS C O doub N N 135 CYS C OXT sing N N 136 CYS CB SG sing N N 137 CYS CB HB2 sing N N 138 CYS CB HB3 sing N N 139 CYS SG HG sing N N 140 CYS OXT HXT sing N N 141 GLN N CA sing N N 142 GLN N H sing N N 143 GLN N H2 sing N N 144 GLN CA C sing N N 145 GLN CA CB sing N N 146 GLN CA HA sing N N 147 GLN C O doub N N 148 GLN C OXT sing N N 149 GLN CB CG sing N N 150 GLN CB HB2 sing N N 151 GLN CB HB3 sing N N 152 GLN CG CD sing N N 153 GLN CG HG2 sing N N 154 GLN CG HG3 sing N N 155 GLN CD OE1 doub N N 156 GLN CD NE2 sing N N 157 GLN NE2 HE21 sing N N 158 GLN NE2 HE22 sing N N 159 GLN OXT HXT sing N N 160 GLU N CA sing N N 161 GLU N H sing N N 162 GLU N H2 sing N N 163 GLU CA C sing N N 164 GLU CA CB sing N N 165 GLU CA HA sing N N 166 GLU C O doub N N 167 GLU C OXT sing N N 168 GLU CB CG sing N N 169 GLU CB HB2 sing N N 170 GLU CB HB3 sing N N 171 GLU CG CD sing N N 172 GLU CG HG2 sing N N 173 GLU CG HG3 sing N N 174 GLU CD OE1 doub N N 175 GLU CD OE2 sing N N 176 GLU OE2 HE2 sing N N 177 GLU OXT HXT sing N N 178 GLY N CA sing N N 179 GLY N H sing N N 180 GLY N H2 sing N N 181 GLY CA C sing N N 182 GLY CA HA2 sing N N 183 GLY CA HA3 sing N N 184 GLY C O doub N N 185 GLY C OXT sing N N 186 GLY OXT HXT sing N N 187 HIS N CA sing N N 188 HIS N H sing N N 189 HIS N H2 sing N N 190 HIS CA C sing N N 191 HIS CA CB sing N N 192 HIS CA HA sing N N 193 HIS C O doub N N 194 HIS C OXT sing N N 195 HIS CB CG sing N N 196 HIS CB HB2 sing N N 197 HIS CB HB3 sing N N 198 HIS CG ND1 sing Y N 199 HIS CG CD2 doub Y N 200 HIS ND1 CE1 doub Y N 201 HIS ND1 HD1 sing N N 202 HIS CD2 NE2 sing Y N 203 HIS CD2 HD2 sing N N 204 HIS CE1 NE2 sing Y N 205 HIS CE1 HE1 sing N N 206 HIS NE2 HE2 sing N N 207 HIS OXT HXT sing N N 208 HOH O H1 sing N N 209 HOH O H2 sing N N 210 ILE N CA sing N N 211 ILE N H sing N N 212 ILE N H2 sing N N 213 ILE CA C sing N N 214 ILE CA CB sing N N 215 ILE CA HA sing N N 216 ILE C O doub N N 217 ILE C OXT sing N N 218 ILE CB CG1 sing N N 219 ILE CB CG2 sing N N 220 ILE CB HB sing N N 221 ILE CG1 CD1 sing N N 222 ILE CG1 HG12 sing N N 223 ILE CG1 HG13 sing N N 224 ILE CG2 HG21 sing N N 225 ILE CG2 HG22 sing N N 226 ILE CG2 HG23 sing N N 227 ILE CD1 HD11 sing N N 228 ILE CD1 HD12 sing N N 229 ILE CD1 HD13 sing N N 230 ILE OXT HXT sing N N 231 LEU N CA sing N N 232 LEU N H sing N N 233 LEU N H2 sing N N 234 LEU CA C sing N N 235 LEU CA CB sing N N 236 LEU CA HA sing N N 237 LEU C O doub N N 238 LEU C OXT sing N N 239 LEU CB CG sing N N 240 LEU CB HB2 sing N N 241 LEU CB HB3 sing N N 242 LEU CG CD1 sing N N 243 LEU CG CD2 sing N N 244 LEU CG HG sing N N 245 LEU CD1 HD11 sing N N 246 LEU CD1 HD12 sing N N 247 LEU CD1 HD13 sing N N 248 LEU CD2 HD21 sing N N 249 LEU CD2 HD22 sing N N 250 LEU CD2 HD23 sing N N 251 LEU OXT HXT sing N N 252 LYS N CA sing N N 253 LYS N H sing N N 254 LYS N H2 sing N N 255 LYS CA C sing N N 256 LYS CA CB sing N N 257 LYS CA HA sing N N 258 LYS C O doub N N 259 LYS C OXT sing N N 260 LYS CB CG sing N N 261 LYS CB HB2 sing N N 262 LYS CB HB3 sing N N 263 LYS CG CD sing N N 264 LYS CG HG2 sing N N 265 LYS CG HG3 sing N N 266 LYS CD CE sing N N 267 LYS CD HD2 sing N N 268 LYS CD HD3 sing N N 269 LYS CE NZ sing N N 270 LYS CE HE2 sing N N 271 LYS CE HE3 sing N N 272 LYS NZ HZ1 sing N N 273 LYS NZ HZ2 sing N N 274 LYS NZ HZ3 sing N N 275 LYS OXT HXT sing N N 276 PHE N CA sing N N 277 PHE N H sing N N 278 PHE N H2 sing N N 279 PHE CA C sing N N 280 PHE CA CB sing N N 281 PHE CA HA sing N N 282 PHE C O doub N N 283 PHE C OXT sing N N 284 PHE CB CG sing N N 285 PHE CB HB2 sing N N 286 PHE CB HB3 sing N N 287 PHE CG CD1 doub Y N 288 PHE CG CD2 sing Y N 289 PHE CD1 CE1 sing Y N 290 PHE CD1 HD1 sing N N 291 PHE CD2 CE2 doub Y N 292 PHE CD2 HD2 sing N N 293 PHE CE1 CZ doub Y N 294 PHE CE1 HE1 sing N N 295 PHE CE2 CZ sing Y N 296 PHE CE2 HE2 sing N N 297 PHE CZ HZ sing N N 298 PHE OXT HXT sing N N 299 PRO N CA sing N N 300 PRO N CD sing N N 301 PRO N H sing N N 302 PRO CA C sing N N 303 PRO CA CB sing N N 304 PRO CA HA sing N N 305 PRO C O doub N N 306 PRO C OXT sing N N 307 PRO CB CG sing N N 308 PRO CB HB2 sing N N 309 PRO CB HB3 sing N N 310 PRO CG CD sing N N 311 PRO CG HG2 sing N N 312 PRO CG HG3 sing N N 313 PRO CD HD2 sing N N 314 PRO CD HD3 sing N N 315 PRO OXT HXT sing N N 316 SER N CA sing N N 317 SER N H sing N N 318 SER N H2 sing N N 319 SER CA C sing N N 320 SER CA CB sing N N 321 SER CA HA sing N N 322 SER C O doub N N 323 SER C OXT sing N N 324 SER CB OG sing N N 325 SER CB HB2 sing N N 326 SER CB HB3 sing N N 327 SER OG HG sing N N 328 SER OXT HXT sing N N 329 THR N CA sing N N 330 THR N H sing N N 331 THR N H2 sing N N 332 THR CA C sing N N 333 THR CA CB sing N N 334 THR CA HA sing N N 335 THR C O doub N N 336 THR C OXT sing N N 337 THR CB OG1 sing N N 338 THR CB CG2 sing N N 339 THR CB HB sing N N 340 THR OG1 HG1 sing N N 341 THR CG2 HG21 sing N N 342 THR CG2 HG22 sing N N 343 THR CG2 HG23 sing N N 344 THR OXT HXT sing N N 345 TRP N CA sing N N 346 TRP N H sing N N 347 TRP N H2 sing N N 348 TRP CA C sing N N 349 TRP CA CB sing N N 350 TRP CA HA sing N N 351 TRP C O doub N N 352 TRP C OXT sing N N 353 TRP CB CG sing N N 354 TRP CB HB2 sing N N 355 TRP CB HB3 sing N N 356 TRP CG CD1 doub Y N 357 TRP CG CD2 sing Y N 358 TRP CD1 NE1 sing Y N 359 TRP CD1 HD1 sing N N 360 TRP CD2 CE2 doub Y N 361 TRP CD2 CE3 sing Y N 362 TRP NE1 CE2 sing Y N 363 TRP NE1 HE1 sing N N 364 TRP CE2 CZ2 sing Y N 365 TRP CE3 CZ3 doub Y N 366 TRP CE3 HE3 sing N N 367 TRP CZ2 CH2 doub Y N 368 TRP CZ2 HZ2 sing N N 369 TRP CZ3 CH2 sing Y N 370 TRP CZ3 HZ3 sing N N 371 TRP CH2 HH2 sing N N 372 TRP OXT HXT sing N N 373 TYR N CA sing N N 374 TYR N H sing N N 375 TYR N H2 sing N N 376 TYR CA C sing N N 377 TYR CA CB sing N N 378 TYR CA HA sing N N 379 TYR C O doub N N 380 TYR C OXT sing N N 381 TYR CB CG sing N N 382 TYR CB HB2 sing N N 383 TYR CB HB3 sing N N 384 TYR CG CD1 doub Y N 385 TYR CG CD2 sing Y N 386 TYR CD1 CE1 sing Y N 387 TYR CD1 HD1 sing N N 388 TYR CD2 CE2 doub Y N 389 TYR CD2 HD2 sing N N 390 TYR CE1 CZ doub Y N 391 TYR CE1 HE1 sing N N 392 TYR CE2 CZ sing Y N 393 TYR CE2 HE2 sing N N 394 TYR CZ OH sing N N 395 TYR OH HH sing N N 396 TYR OXT HXT sing N N 397 VAL N CA sing N N 398 VAL N H sing N N 399 VAL N H2 sing N N 400 VAL CA C sing N N 401 VAL CA CB sing N N 402 VAL CA HA sing N N 403 VAL C O doub N N 404 VAL C OXT sing N N 405 VAL CB CG1 sing N N 406 VAL CB CG2 sing N N 407 VAL CB HB sing N N 408 VAL CG1 HG11 sing N N 409 VAL CG1 HG12 sing N N 410 VAL CG1 HG13 sing N N 411 VAL CG2 HG21 sing N N 412 VAL CG2 HG22 sing N N 413 VAL CG2 HG23 sing N N 414 VAL OXT HXT sing N N 415 # _em_3d_crystal_entity.angle_alpha 90 _em_3d_crystal_entity.angle_beta 90 _em_3d_crystal_entity.angle_gamma 90 _em_3d_crystal_entity.image_processing_id 1 _em_3d_crystal_entity.id 1 _em_3d_crystal_entity.length_a 42.31 _em_3d_crystal_entity.length_b 48.32 _em_3d_crystal_entity.length_c 100.48 _em_3d_crystal_entity.space_group_name 'P 21 21 21' _em_3d_crystal_entity.space_group_num 19 # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type NONE # _em_diffraction_shell.em_diffraction_stats_id 1 _em_diffraction_shell.fourier_space_coverage 91.2 _em_diffraction_shell.high_resolution 2.5 _em_diffraction_shell.id 1 _em_diffraction_shell.low_resolution 2.6 _em_diffraction_shell.multiplicity 3.8 _em_diffraction_shell.num_structure_factors 742 _em_diffraction_shell.phase_residual 28.9 # _em_diffraction_stats.details ? _em_diffraction_stats.fourier_space_coverage 87.7 _em_diffraction_stats.high_resolution 2.5 _em_diffraction_stats.id 1 _em_diffraction_stats.image_processing_id 1 _em_diffraction_stats.num_intensities_measured 24784 _em_diffraction_stats.num_structure_factors 6665 _em_diffraction_stats.overall_phase_error ? _em_diffraction_stats.overall_phase_residual ? _em_diffraction_stats.phase_error_rejection_criteria NULL _em_diffraction_stats.r_merge 24.9 _em_diffraction_stats.r_sym ? # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.ncbi_tax_id 3649 _em_entity_assembly_naturalsource.organism 'Carica papaya' _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? _em_entity_assembly_naturalsource.details ? # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time ? _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 0.045 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'DIRECT ELECTRON APOLLO (4k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.category _em_software.details _em_software.id _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id _em_software.name _em_software.version 'IMAGE ACQUISITION' ? 1 ? ? 1 ? ? MASKING ? 2 ? ? ? ? ? 'CTF CORRECTION' ? 3 1 ? ? ? ? 'LAYERLINE INDEXING' ? 4 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 5 ? ? ? ? ? 'MODEL FITTING' ? 6 ? 1 ? ? ? OTHER ? 7 ? ? ? ? ? 'MOLECULAR REPLACEMENT' ? 8 1 ? ? ? ? 'LATTICE DISTORTION CORRECTION' ? 9 1 ? ? ? ? 'SYMMETRY DETERMINATION' ? 10 1 ? ? ? ? 'CRYSTALLOGRAPHY MERGING' ? 11 1 ? ? ? ? RECONSTRUCTION ? 12 1 ? ? ? ? 'MODEL REFINEMENT' ? 13 ? 1 ? ? ? 'PARTICLE SELECTION' ? 14 1 1 1 ? ? 'VOLUME SELECTION' ? 15 1 1 1 ? ? CLASSIFICATION ? 16 1 1 1 ? ? 'INITIAL EULER ASSIGNMENT' ? 17 1 1 1 ? ? 'FINAL EULER ASSIGNMENT' ? 18 1 1 1 ? ? 'SERIES ALIGNMENT' ? 19 1 1 1 ? ? # _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Science Foundation (NSF, United States)' 'United States' DMR-1548924 1 'Department of Energy (DOE, United States)' 'United States' DE-FC02-02ER63421 2 'Howard Hughes Medical Institute (HHMI)' 'United States' HHMI-EPI 3 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 9PAP _pdbx_initial_refinement_model.details ? # _atom_sites.entry_id 9NAO _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.023635 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.020695 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.009952 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O S # loop_ #