data_9KL3 # _entry.id 9KL3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.408 _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 9KL3 pdb_00009kl3 10.2210/pdb9kl3/pdb WWPDB D_1300050751 ? ? EMDB EMD-62399 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date _pdbx_audit_revision_history.part_number 1 'Structure model' 1 0 2025-11-19 ? 2 'EM metadata' 1 0 2025-11-19 ? 3 'Additional map' 1 0 2025-11-19 1 4 FSC 1 0 2025-11-19 ? 5 'Half map' 1 0 2025-11-19 1 6 'Half map' 1 0 2025-11-19 2 7 Image 1 0 2025-11-19 ? 8 Mask 1 0 2025-11-19 1 9 'Primary map' 1 0 2025-11-19 ? 10 'Structure model' 1 1 2025-12-17 ? 11 'EM metadata' 1 1 2025-12-17 ? 12 'Structure model' 1 2 2025-12-31 ? 13 'EM metadata' 1 2 2025-12-31 ? # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 2 'EM metadata' repository 'Initial release' ? ? 3 3 'Additional map' repository 'Initial release' ? ? 4 4 FSC repository 'Initial release' ? ? 5 5 'Half map' repository 'Initial release' ? ? 6 6 'Half map' repository 'Initial release' ? ? 7 7 Image repository 'Initial release' ? ? 8 8 Mask repository 'Initial release' ? ? 9 9 'Primary map' repository 'Initial release' ? ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 10 'Structure model' 'Data collection' 2 10 'Structure model' 'Database references' 3 11 'EM metadata' 'Database references' 4 11 'EM metadata' 'Experimental summary' 5 12 'Structure model' 'Data collection' 6 12 'Structure model' 'Database references' 7 13 'EM metadata' 'Database references' 8 13 'EM metadata' 'Experimental summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 10 'Structure model' citation 2 10 'Structure model' citation_author 3 10 'Structure model' em_admin 4 11 'EM metadata' citation 5 11 'EM metadata' citation_author 6 11 'EM metadata' em_admin 7 12 'Structure model' citation 8 12 'Structure model' em_admin 9 13 'EM metadata' citation 10 13 'EM metadata' em_admin # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 10 'Structure model' '_citation.country' 2 10 'Structure model' '_citation.journal_abbrev' 3 10 'Structure model' '_citation.journal_id_CSD' 4 10 'Structure model' '_citation.journal_id_ISSN' 5 10 'Structure model' '_citation.pdbx_database_id_DOI' 6 10 'Structure model' '_citation.pdbx_database_id_PubMed' 7 10 'Structure model' '_citation.title' 8 10 'Structure model' '_citation.year' 9 10 'Structure model' '_citation_author.identifier_ORCID' 10 10 'Structure model' '_citation_author.name' 11 10 'Structure model' '_em_admin.last_update' 12 11 'EM metadata' '_citation.country' 13 11 'EM metadata' '_citation.journal_abbrev' 14 11 'EM metadata' '_citation.journal_id_CSD' 15 11 'EM metadata' '_citation.journal_id_ISSN' 16 11 'EM metadata' '_citation.pdbx_database_id_DOI' 17 11 'EM metadata' '_citation.pdbx_database_id_PubMed' 18 11 'EM metadata' '_citation.title' 19 11 'EM metadata' '_citation.year' 20 11 'EM metadata' '_citation_author.identifier_ORCID' 21 11 'EM metadata' '_citation_author.name' 22 11 'EM metadata' '_em_admin.last_update' 23 12 'Structure model' '_citation.journal_volume' 24 12 'Structure model' '_em_admin.last_update' 25 13 'EM metadata' '_citation.journal_volume' 26 13 'EM metadata' '_em_admin.last_update' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9KL3 _pdbx_database_status.recvd_initial_deposition_date 2024-11-14 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _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 Y # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'CryoEM structure of Pleurocybella porrigens lectin (PPL) in complex with GalNAc' _pdbx_database_related.db_id EMD-62399 _pdbx_database_related.content_type 'associated EM volume' # loop_ _pdbx_contact_author.id _pdbx_contact_author.email _pdbx_contact_author.name_first _pdbx_contact_author.name_last _pdbx_contact_author.name_mi _pdbx_contact_author.role _pdbx_contact_author.identifier_ORCID 3 jtame@yokohama-cu.ac.jp Jeremy Tame R.H. 'principal investigator/group leader' 0000-0002-9341-7280 4 w175502f@yokohama-cu.ac.jp Kamata Kenichi ? 'principal investigator/group leader' 0000-0003-4344-8473 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Ishimoto, N.' 1 0000-0001-8976-8582 'Adachi, D.' 2 0009-0000-0536-758X 'Kawabata, H.' 3 0000-0001-7495-4219 'Park, S.Y.' 4 0000-0001-6164-8896 'Tame, J.R.H.' 5 0000-0002-9341-7280 'Kamata, K.' 6 0000-0003-4344-8473 # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Glycobiology _citation.journal_id_ASTM ? _citation.journal_id_CSD 9999 _citation.journal_id_ISSN 1460-2423 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 36 _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Crystal and Cryo-EM structure of PPL, a novel hexameric R-type lectin from the poisonous mushroom Pleurocybella porrigens.' _citation.year 2025 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/glycob/cwaf082 _citation.pdbx_database_id_PubMed 41342409 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Adachi, D.' 1 ? primary 'Ishimoto, N.' 2 ? primary 'Mizutani, K.' 3 ? primary 'Takahashi, K.' 4 ? primary 'Kubota, R.' 5 ? primary 'Kawabata, H.' 6 ? primary 'Park, S.Y.' 7 ? primary 'Vandebroek, L.' 8 ? primary 'Voet, A.R.D.' 9 ? primary 'Yamada, M.' 10 ? primary 'Ozeki, Y.' 11 ? primary 'Fujii, Y.' 12 ? primary 'Fujita, H.' 13 ? primary 'Tame, J.R.H.' 14 ? primary 'Kamata, K.' 15 0000-0003-4344-8473 # 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 man Lectin 14625.118 1 ? ? ? ? 2 non-polymer syn 2-acetamido-2-deoxy-alpha-D-galactopyranose 221.208 1 ? ? ? ? # _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 ;GSHMSIPAGTYLIRNVESNLYLDLRGSNPAPGTDAIVWGRTGNNNQRWIVTTHSDGTRTLETVGINSSAFIATIQPGGRV TGHPNNETRLTITNVNPGEYSISAGGLLWLANTPVGGTGEAVTLQAAGGAAQSLWVFEAV ; _entity_poly.pdbx_seq_one_letter_code_can ;GSHMSIPAGTYLIRNVESNLYLDLRGSNPAPGTDAIVWGRTGNNNQRWIVTTHSDGTRTLETVGINSSAFIATIQPGGRV TGHPNNETRLTITNVNPGEYSISAGGLLWLANTPVGGTGEAVTLQAAGGAAQSLWVFEAV ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 2-acetamido-2-deoxy-alpha-D-galactopyranose _pdbx_entity_nonpoly.comp_id A2G # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 SER n 1 3 HIS n 1 4 MET n 1 5 SER n 1 6 ILE n 1 7 PRO n 1 8 ALA n 1 9 GLY n 1 10 THR n 1 11 TYR n 1 12 LEU n 1 13 ILE n 1 14 ARG n 1 15 ASN n 1 16 VAL n 1 17 GLU n 1 18 SER n 1 19 ASN n 1 20 LEU n 1 21 TYR n 1 22 LEU n 1 23 ASP n 1 24 LEU n 1 25 ARG n 1 26 GLY n 1 27 SER n 1 28 ASN n 1 29 PRO n 1 30 ALA n 1 31 PRO n 1 32 GLY n 1 33 THR n 1 34 ASP n 1 35 ALA n 1 36 ILE n 1 37 VAL n 1 38 TRP n 1 39 GLY n 1 40 ARG n 1 41 THR n 1 42 GLY n 1 43 ASN n 1 44 ASN n 1 45 ASN n 1 46 GLN n 1 47 ARG n 1 48 TRP n 1 49 ILE n 1 50 VAL n 1 51 THR n 1 52 THR n 1 53 HIS n 1 54 SER n 1 55 ASP n 1 56 GLY n 1 57 THR n 1 58 ARG n 1 59 THR n 1 60 LEU n 1 61 GLU n 1 62 THR n 1 63 VAL n 1 64 GLY n 1 65 ILE n 1 66 ASN n 1 67 SER n 1 68 SER n 1 69 ALA n 1 70 PHE n 1 71 ILE n 1 72 ALA n 1 73 THR n 1 74 ILE n 1 75 GLN n 1 76 PRO n 1 77 GLY n 1 78 GLY n 1 79 ARG n 1 80 VAL n 1 81 THR n 1 82 GLY n 1 83 HIS n 1 84 PRO n 1 85 ASN n 1 86 ASN n 1 87 GLU n 1 88 THR n 1 89 ARG n 1 90 LEU n 1 91 THR n 1 92 ILE n 1 93 THR n 1 94 ASN n 1 95 VAL n 1 96 ASN n 1 97 PRO n 1 98 GLY n 1 99 GLU n 1 100 TYR n 1 101 SER n 1 102 ILE n 1 103 SER n 1 104 ALA n 1 105 GLY n 1 106 GLY n 1 107 LEU n 1 108 LEU n 1 109 TRP n 1 110 LEU n 1 111 ALA n 1 112 ASN n 1 113 THR n 1 114 PRO n 1 115 VAL n 1 116 GLY n 1 117 GLY n 1 118 THR n 1 119 GLY n 1 120 GLU n 1 121 ALA n 1 122 VAL n 1 123 THR n 1 124 LEU n 1 125 GLN n 1 126 ALA n 1 127 ALA n 1 128 GLY n 1 129 GLY n 1 130 ALA n 1 131 ALA n 1 132 GLN n 1 133 SER n 1 134 LEU n 1 135 TRP n 1 136 VAL n 1 137 PHE n 1 138 GLU n 1 139 ALA n 1 140 VAL n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 140 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Pleurocybella porrigens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 71910 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # 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 A2G 'D-saccharide, alpha linking' . 2-acetamido-2-deoxy-alpha-D-galactopyranose ;N-acetyl-alpha-D-galactosamine; 2-acetamido-2-deoxy-alpha-D-galactose; 2-acetamido-2-deoxy-D-galactose; 2-acetamido-2-deoxy-galactose; N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE ; 'C8 H15 N O6' 221.208 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 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 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 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_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier A2G 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGalpNAca A2G 'COMMON NAME' GMML 1.0 N-acetyl-a-D-galactopyranosamine A2G 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-GalpNAc A2G 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GalNAc # 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 GLY 1 -2 ? ? ? A . n A 1 2 SER 2 -1 ? ? ? A . n A 1 3 HIS 3 0 ? ? ? A . n A 1 4 MET 4 1 1 MET MET A . n A 1 5 SER 5 2 2 SER SER A . n A 1 6 ILE 6 3 3 ILE ILE A . n A 1 7 PRO 7 4 4 PRO PRO A . n A 1 8 ALA 8 5 5 ALA ALA A . n A 1 9 GLY 9 6 6 GLY GLY A . n A 1 10 THR 10 7 7 THR THR A . n A 1 11 TYR 11 8 8 TYR TYR A . n A 1 12 LEU 12 9 9 LEU LEU A . n A 1 13 ILE 13 10 10 ILE ILE A . n A 1 14 ARG 14 11 11 ARG ARG A . n A 1 15 ASN 15 12 12 ASN ASN A . n A 1 16 VAL 16 13 13 VAL VAL A . n A 1 17 GLU 17 14 14 GLU GLU A . n A 1 18 SER 18 15 15 SER SER A . n A 1 19 ASN 19 16 16 ASN ASN A . n A 1 20 LEU 20 17 17 LEU LEU A . n A 1 21 TYR 21 18 18 TYR TYR A . n A 1 22 LEU 22 19 19 LEU LEU A . n A 1 23 ASP 23 20 20 ASP ASP A . n A 1 24 LEU 24 21 21 LEU LEU A . n A 1 25 ARG 25 22 22 ARG ARG A . n A 1 26 GLY 26 23 23 GLY GLY A . n A 1 27 SER 27 24 24 SER SER A . n A 1 28 ASN 28 25 25 ASN ASN A . n A 1 29 PRO 29 26 26 PRO PRO A . n A 1 30 ALA 30 27 27 ALA ALA A . n A 1 31 PRO 31 28 28 PRO PRO A . n A 1 32 GLY 32 29 29 GLY GLY A . n A 1 33 THR 33 30 30 THR THR A . n A 1 34 ASP 34 31 31 ASP ASP A . n A 1 35 ALA 35 32 32 ALA ALA A . n A 1 36 ILE 36 33 33 ILE ILE A . n A 1 37 VAL 37 34 34 VAL VAL A . n A 1 38 TRP 38 35 35 TRP TRP A . n A 1 39 GLY 39 36 36 GLY GLY A . n A 1 40 ARG 40 37 37 ARG ARG A . n A 1 41 THR 41 38 38 THR THR A . n A 1 42 GLY 42 39 39 GLY GLY A . n A 1 43 ASN 43 40 40 ASN ASN A . n A 1 44 ASN 44 41 41 ASN ASN A . n A 1 45 ASN 45 42 42 ASN ASN A . n A 1 46 GLN 46 43 43 GLN GLN A . n A 1 47 ARG 47 44 44 ARG ARG A . n A 1 48 TRP 48 45 45 TRP TRP A . n A 1 49 ILE 49 46 46 ILE ILE A . n A 1 50 VAL 50 47 47 VAL VAL A . n A 1 51 THR 51 48 48 THR THR A . n A 1 52 THR 52 49 49 THR THR A . n A 1 53 HIS 53 50 50 HIS HIS A . n A 1 54 SER 54 51 51 SER SER A . n A 1 55 ASP 55 52 52 ASP ASP A . n A 1 56 GLY 56 53 53 GLY GLY A . n A 1 57 THR 57 54 54 THR THR A . n A 1 58 ARG 58 55 55 ARG ARG A . n A 1 59 THR 59 56 56 THR THR A . n A 1 60 LEU 60 57 57 LEU LEU A . n A 1 61 GLU 61 58 58 GLU GLU A . n A 1 62 THR 62 59 59 THR THR A . n A 1 63 VAL 63 60 60 VAL VAL A . n A 1 64 GLY 64 61 61 GLY GLY A . n A 1 65 ILE 65 62 62 ILE ILE A . n A 1 66 ASN 66 63 63 ASN ASN A . n A 1 67 SER 67 64 64 SER SER A . n A 1 68 SER 68 65 65 SER SER A . n A 1 69 ALA 69 66 66 ALA ALA A . n A 1 70 PHE 70 67 67 PHE PHE A . n A 1 71 ILE 71 68 68 ILE ILE A . n A 1 72 ALA 72 69 69 ALA ALA A . n A 1 73 THR 73 70 70 THR THR A . n A 1 74 ILE 74 71 71 ILE ILE A . n A 1 75 GLN 75 72 72 GLN GLN A . n A 1 76 PRO 76 73 73 PRO PRO A . n A 1 77 GLY 77 74 74 GLY GLY A . n A 1 78 GLY 78 75 75 GLY GLY A . n A 1 79 ARG 79 76 76 ARG ARG A . n A 1 80 VAL 80 77 77 VAL VAL A . n A 1 81 THR 81 78 78 THR THR A . n A 1 82 GLY 82 79 79 GLY GLY A . n A 1 83 HIS 83 80 80 HIS HIS A . n A 1 84 PRO 84 81 81 PRO PRO A . n A 1 85 ASN 85 82 82 ASN ASN A . n A 1 86 ASN 86 83 83 ASN ASN A . n A 1 87 GLU 87 84 84 GLU GLU A . n A 1 88 THR 88 85 85 THR THR A . n A 1 89 ARG 89 86 86 ARG ARG A . n A 1 90 LEU 90 87 87 LEU LEU A . n A 1 91 THR 91 88 88 THR THR A . n A 1 92 ILE 92 89 89 ILE ILE A . n A 1 93 THR 93 90 90 THR THR A . n A 1 94 ASN 94 91 91 ASN ASN A . n A 1 95 VAL 95 92 92 VAL VAL A . n A 1 96 ASN 96 93 93 ASN ASN A . n A 1 97 PRO 97 94 94 PRO PRO A . n A 1 98 GLY 98 95 95 GLY GLY A . n A 1 99 GLU 99 96 96 GLU GLU A . n A 1 100 TYR 100 97 97 TYR TYR A . n A 1 101 SER 101 98 98 SER SER A . n A 1 102 ILE 102 99 99 ILE ILE A . n A 1 103 SER 103 100 100 SER SER A . n A 1 104 ALA 104 101 101 ALA ALA A . n A 1 105 GLY 105 102 102 GLY GLY A . n A 1 106 GLY 106 103 103 GLY GLY A . n A 1 107 LEU 107 104 104 LEU LEU A . n A 1 108 LEU 108 105 105 LEU LEU A . n A 1 109 TRP 109 106 106 TRP TRP A . n A 1 110 LEU 110 107 107 LEU LEU A . n A 1 111 ALA 111 108 108 ALA ALA A . n A 1 112 ASN 112 109 109 ASN ASN A . n A 1 113 THR 113 110 110 THR THR A . n A 1 114 PRO 114 111 111 PRO PRO A . n A 1 115 VAL 115 112 112 VAL VAL A . n A 1 116 GLY 116 113 113 GLY GLY A . n A 1 117 GLY 117 114 114 GLY GLY A . n A 1 118 THR 118 115 115 THR THR A . n A 1 119 GLY 119 116 116 GLY GLY A . n A 1 120 GLU 120 117 117 GLU GLU A . n A 1 121 ALA 121 118 118 ALA ALA A . n A 1 122 VAL 122 119 119 VAL VAL A . n A 1 123 THR 123 120 120 THR THR A . n A 1 124 LEU 124 121 121 LEU LEU A . n A 1 125 GLN 125 122 122 GLN GLN A . n A 1 126 ALA 126 123 123 ALA ALA A . n A 1 127 ALA 127 124 124 ALA ALA A . n A 1 128 GLY 128 125 125 GLY GLY A . n A 1 129 GLY 129 126 126 GLY GLY A . n A 1 130 ALA 130 127 127 ALA ALA A . n A 1 131 ALA 131 128 128 ALA ALA A . n A 1 132 GLN 132 129 129 GLN GLN A . n A 1 133 SER 133 130 130 SER SER A . n A 1 134 LEU 134 131 131 LEU LEU A . n A 1 135 TRP 135 132 132 TRP TRP A . n A 1 136 VAL 136 133 133 VAL VAL A . n A 1 137 PHE 137 134 134 PHE PHE A . n A 1 138 GLU 138 135 135 GLU GLU A . n A 1 139 ALA 139 136 136 ALA ALA A . n A 1 140 VAL 140 137 137 VAL VAL A . n # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id A2G _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 201 _pdbx_nonpoly_scheme.auth_seq_num 201 _pdbx_nonpoly_scheme.pdb_mon_id A2G _pdbx_nonpoly_scheme.auth_mon_id A2G _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _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 9KL3 _cell.details ? _cell.formula_units_Z ? _cell.length_a 1.00 _cell.length_a_esd ? _cell.length_b 1.00 _cell.length_b_esd ? _cell.length_c 1.00 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB ? _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 9KL3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _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 9KL3 _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 9KL3 _refine.pdbx_diffrn_id ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low ? _refine.ls_d_res_high . _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # 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 MICROSCOPY' ? 0.002 ? 6282 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.407 ? 8616 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 3.593 ? 876 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.042 ? 1020 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.006 ? 1122 ? f_plane_restr ? ? # _struct.entry_id 9KL3 _struct.title 'CryoEM structure of Pleurocybella porrigens lectin (PPL) in complex with GalNAc' _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 9KL3 _struct_keywords.text 'trefoil, lectin, SUGAR BINDING PROTEIN' _struct_keywords.pdbx_keywords 'SUGAR BINDING PROTEIN' # 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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code B6ZK51_9AGAR _struct_ref.pdbx_db_accession B6ZK51 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSIPAGTYLIRNVESNLYLDLRGSNPAPGTDAIVWGRTGNNNQRWIVTTHSDGTRTLETVGINSSAFIATIQPGGRVTGH PNNETRLTITNVNPGEYSISAGGLLWLANTPVGGTGEAVTLQAAGGAAQSLWVFEAV ; _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 9KL3 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 4 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 140 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession B6ZK51 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 137 _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 137 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 9KL3 GLY A 1 ? UNP B6ZK51 ? ? 'expression tag' -2 1 1 9KL3 SER A 2 ? UNP B6ZK51 ? ? 'expression tag' -1 2 1 9KL3 HIS A 3 ? UNP B6ZK51 ? ? 'expression tag' 0 3 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details AUC # _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 ? _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 # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id AA1 _struct_conf.beg_label_comp_id GLY _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 26 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id ASN _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 28 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id GLY _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 23 _struct_conf.end_auth_comp_id ASN _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 25 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 3 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 6 ? AA2 ? 4 ? AA3 ? 3 ? # 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 AA1 3 4 ? anti-parallel AA1 4 5 ? anti-parallel AA1 5 6 ? anti-parallel AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel AA2 3 4 ? anti-parallel AA3 1 2 ? anti-parallel AA3 2 3 ? 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 ARG A 58 ? THR A 62 ? ARG A 55 THR A 59 AA1 2 TRP A 48 ? THR A 52 ? TRP A 45 THR A 49 AA1 3 GLY A 9 ? ASN A 15 ? GLY A 6 ASN A 12 AA1 4 LEU A 20 ? LEU A 24 ? LEU A 17 LEU A 21 AA1 5 THR A 33 ? TRP A 38 ? THR A 30 TRP A 35 AA1 6 THR A 81 ? GLY A 82 ? THR A 78 GLY A 79 AA2 1 ARG A 58 ? THR A 62 ? ARG A 55 THR A 59 AA2 2 TRP A 48 ? THR A 52 ? TRP A 45 THR A 49 AA2 3 GLY A 9 ? ASN A 15 ? GLY A 6 ASN A 12 AA2 4 TRP A 135 ? ALA A 139 ? TRP A 132 ALA A 136 AA3 1 THR A 91 ? ASN A 94 ? THR A 88 ASN A 91 AA3 2 TYR A 100 ? ALA A 104 ? TYR A 97 ALA A 101 AA3 3 LEU A 107 ? LEU A 108 ? LEU A 104 LEU A 105 # 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 O GLU A 61 ? O GLU A 58 N ILE A 49 ? N ILE A 46 AA1 2 3 O VAL A 50 ? O VAL A 47 N GLY A 9 ? N GLY A 6 AA1 3 4 N ASN A 15 ? N ASN A 12 O LEU A 20 ? O LEU A 17 AA1 4 5 N ASP A 23 ? N ASP A 20 O ILE A 36 ? O ILE A 33 AA1 5 6 N THR A 33 ? N THR A 30 O GLY A 82 ? O GLY A 79 AA2 1 2 O GLU A 61 ? O GLU A 58 N ILE A 49 ? N ILE A 46 AA2 2 3 O VAL A 50 ? O VAL A 47 N GLY A 9 ? N GLY A 6 AA2 3 4 N LEU A 12 ? N LEU A 9 O GLU A 138 ? O GLU A 135 AA3 1 2 N THR A 91 ? N THR A 88 O SER A 103 ? O SER A 100 AA3 2 3 N ALA A 104 ? N ALA A 101 O LEU A 107 ? O LEU A 104 # _pdbx_entry_details.entry_id 9KL3 _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 N _pdbx_entry_details.has_protein_modification N # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id ASN _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 40 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -79.75 _pdbx_validate_torsion.psi -169.79 # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9KL3 _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_reconstruction.entry_id 9KL3 _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 3.24 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.num_particles 74285 _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages 1 _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type POINT # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details ? _em_buffer.pH 8.0 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type COMPLEX _em_entity_assembly.name 'Pleurocybella porrigens lectin in complex with GalNac' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 9KL3 _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'FEI TALOS ARCTICA' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model 'FEI TITAN KRIOS AUTOGRID HOLDER' _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 200 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_min 800 _em_imaging.nominal_defocus_max 1800 _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 ? _em_imaging.recording_temperature_maximum ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.specimen_id 1 _em_imaging.cryogen NITROGEN # _em_sample_support.id 1 _em_sample_support.film_material ? _em_sample_support.method ? _em_sample_support.grid_material COPPER _em_sample_support.grid_mesh_size 300 _em_sample_support.grid_type 'Quantifoil R1.2/1.3' _em_sample_support.details ? _em_sample_support.specimen_id 1 _em_sample_support.citation_id ? # _em_vitrification.entry_id 9KL3 _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity 100 _em_vitrification.temp ? _em_vitrification.chamber_temperature 278 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 9KL3 _em_experiment.id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.aggregation_state PARTICLE _em_experiment.entity_assembly_id 1 # _em_single_particle_entity.entry_id 9KL3 _em_single_particle_entity.id 1 _em_single_particle_entity.image_processing_id 1 _em_single_particle_entity.point_symmetry D3 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY -2 ? A GLY 1 2 1 Y 1 A SER -1 ? A SER 2 3 1 Y 1 A HIS 0 ? A HIS 3 # 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 A2G O5 O N N 1 A2G C1 C N S 2 A2G O1 O N N 3 A2G C2 C N R 4 A2G N2 N N N 5 A2G C3 C N R 6 A2G O3 O N N 7 A2G C4 C N R 8 A2G O4 O N N 9 A2G C5 C N R 10 A2G C6 C N N 11 A2G O6 O N N 12 A2G C7 C N N 13 A2G O7 O N N 14 A2G C8 C N N 15 A2G H1 H N N 16 A2G HO1 H N N 17 A2G H2 H N N 18 A2G HN2 H N N 19 A2G H3 H N N 20 A2G HO3 H N N 21 A2G H4 H N N 22 A2G HO4 H N N 23 A2G H5 H N N 24 A2G H61 H N N 25 A2G H81 H N N 26 A2G H82 H N N 27 A2G H83 H N N 28 A2G H62 H N N 29 A2G HO6 H N N 30 ALA N N N N 31 ALA CA C N S 32 ALA C C N N 33 ALA O O N N 34 ALA CB C N N 35 ALA OXT O N N 36 ALA H H N N 37 ALA H2 H N N 38 ALA HA H N N 39 ALA HB1 H N N 40 ALA HB2 H N N 41 ALA HB3 H N N 42 ALA HXT H N N 43 ARG N N N N 44 ARG CA C N S 45 ARG C C N N 46 ARG O O N N 47 ARG CB C N N 48 ARG CG C N N 49 ARG CD C N N 50 ARG NE N N N 51 ARG CZ C N N 52 ARG NH1 N N N 53 ARG NH2 N N N 54 ARG OXT O N N 55 ARG H H N N 56 ARG H2 H N N 57 ARG HA H N N 58 ARG HB2 H N N 59 ARG HB3 H N N 60 ARG HG2 H N N 61 ARG HG3 H N N 62 ARG HD2 H N N 63 ARG HD3 H N N 64 ARG HE H N N 65 ARG HH11 H N N 66 ARG HH12 H N N 67 ARG HH21 H N N 68 ARG HH22 H N N 69 ARG HXT H N N 70 ASN N N N N 71 ASN CA C N S 72 ASN C C N N 73 ASN O O N N 74 ASN CB C N N 75 ASN CG C N N 76 ASN OD1 O N N 77 ASN ND2 N N N 78 ASN OXT O N N 79 ASN H H N N 80 ASN H2 H N N 81 ASN HA H N N 82 ASN HB2 H N N 83 ASN HB3 H N N 84 ASN HD21 H N N 85 ASN HD22 H N N 86 ASN HXT H N N 87 ASP N N N N 88 ASP CA C N S 89 ASP C C N N 90 ASP O O N N 91 ASP CB C N N 92 ASP CG C N N 93 ASP OD1 O N N 94 ASP OD2 O N N 95 ASP OXT O N N 96 ASP H H N N 97 ASP H2 H N N 98 ASP HA H N N 99 ASP HB2 H N N 100 ASP HB3 H N N 101 ASP HD2 H N N 102 ASP HXT H N N 103 GLN N N N N 104 GLN CA C N S 105 GLN C C N N 106 GLN O O N N 107 GLN CB C N N 108 GLN CG C N N 109 GLN CD C N N 110 GLN OE1 O N N 111 GLN NE2 N N N 112 GLN OXT O N N 113 GLN H H N N 114 GLN H2 H N N 115 GLN HA H N N 116 GLN HB2 H N N 117 GLN HB3 H N N 118 GLN HG2 H N N 119 GLN HG3 H N N 120 GLN HE21 H N N 121 GLN HE22 H N N 122 GLN HXT H N N 123 GLU N N N N 124 GLU CA C N S 125 GLU C C N N 126 GLU O O N N 127 GLU CB C N N 128 GLU CG C N N 129 GLU CD C N N 130 GLU OE1 O N N 131 GLU OE2 O N N 132 GLU OXT O N N 133 GLU H H N N 134 GLU H2 H N N 135 GLU HA H N N 136 GLU HB2 H N N 137 GLU HB3 H N N 138 GLU HG2 H N N 139 GLU HG3 H N N 140 GLU HE2 H N N 141 GLU HXT H N N 142 GLY N N N N 143 GLY CA C N N 144 GLY C C N N 145 GLY O O N N 146 GLY OXT O N N 147 GLY H H N N 148 GLY H2 H N N 149 GLY HA2 H N N 150 GLY HA3 H N N 151 GLY HXT H N N 152 HIS N N N N 153 HIS CA C N S 154 HIS C C N N 155 HIS O O N N 156 HIS CB C N N 157 HIS CG C Y N 158 HIS ND1 N Y N 159 HIS CD2 C Y N 160 HIS CE1 C Y N 161 HIS NE2 N Y N 162 HIS OXT O N N 163 HIS H H N N 164 HIS H2 H N N 165 HIS HA H N N 166 HIS HB2 H N N 167 HIS HB3 H N N 168 HIS HD1 H N N 169 HIS HD2 H N N 170 HIS HE1 H N N 171 HIS HE2 H N N 172 HIS HXT H N N 173 ILE N N N N 174 ILE CA C N S 175 ILE C C N N 176 ILE O O N N 177 ILE CB C N S 178 ILE CG1 C N N 179 ILE CG2 C N N 180 ILE CD1 C N N 181 ILE OXT O N N 182 ILE H H N N 183 ILE H2 H N N 184 ILE HA H N N 185 ILE HB H N N 186 ILE HG12 H N N 187 ILE HG13 H N N 188 ILE HG21 H N N 189 ILE HG22 H N N 190 ILE HG23 H N N 191 ILE HD11 H N N 192 ILE HD12 H N N 193 ILE HD13 H N N 194 ILE HXT H N N 195 LEU N N N N 196 LEU CA C N S 197 LEU C C N N 198 LEU O O N N 199 LEU CB C N N 200 LEU CG C N N 201 LEU CD1 C N N 202 LEU CD2 C N N 203 LEU OXT O N N 204 LEU H H N N 205 LEU H2 H N N 206 LEU HA H N N 207 LEU HB2 H N N 208 LEU HB3 H N N 209 LEU HG H N N 210 LEU HD11 H N N 211 LEU HD12 H N N 212 LEU HD13 H N N 213 LEU HD21 H N N 214 LEU HD22 H N N 215 LEU HD23 H N N 216 LEU HXT H N N 217 MET N N N N 218 MET CA C N S 219 MET C C N N 220 MET O O N N 221 MET CB C N N 222 MET CG C N N 223 MET SD S N N 224 MET CE C N N 225 MET OXT O N N 226 MET H H N N 227 MET H2 H N N 228 MET HA H N N 229 MET HB2 H N N 230 MET HB3 H N N 231 MET HG2 H N N 232 MET HG3 H N N 233 MET HE1 H N N 234 MET HE2 H N N 235 MET HE3 H N N 236 MET HXT H N N 237 PHE N N N N 238 PHE CA C N S 239 PHE C C N N 240 PHE O O N N 241 PHE CB C N N 242 PHE CG C Y N 243 PHE CD1 C Y N 244 PHE CD2 C Y N 245 PHE CE1 C Y N 246 PHE CE2 C Y N 247 PHE CZ C Y N 248 PHE OXT O N N 249 PHE H H N N 250 PHE H2 H N N 251 PHE HA H N N 252 PHE HB2 H N N 253 PHE HB3 H N N 254 PHE HD1 H N N 255 PHE HD2 H N N 256 PHE HE1 H N N 257 PHE HE2 H N N 258 PHE HZ H N N 259 PHE HXT H N N 260 PRO N N N N 261 PRO CA C N S 262 PRO C C N N 263 PRO O O N N 264 PRO CB C N N 265 PRO CG C N N 266 PRO CD C N N 267 PRO OXT O N N 268 PRO H H N N 269 PRO HA H N N 270 PRO HB2 H N N 271 PRO HB3 H N N 272 PRO HG2 H N N 273 PRO HG3 H N N 274 PRO HD2 H N N 275 PRO HD3 H N N 276 PRO HXT H N N 277 SER N N N N 278 SER CA C N S 279 SER C C N N 280 SER O O N N 281 SER CB C N N 282 SER OG O N N 283 SER OXT O N N 284 SER H H N N 285 SER H2 H N N 286 SER HA H N N 287 SER HB2 H N N 288 SER HB3 H N N 289 SER HG H N N 290 SER HXT H N N 291 THR N N N N 292 THR CA C N S 293 THR C C N N 294 THR O O N N 295 THR CB C N R 296 THR OG1 O N N 297 THR CG2 C N N 298 THR OXT O N N 299 THR H H N N 300 THR H2 H N N 301 THR HA H N N 302 THR HB H N N 303 THR HG1 H N N 304 THR HG21 H N N 305 THR HG22 H N N 306 THR HG23 H N N 307 THR HXT H N N 308 TRP N N N N 309 TRP CA C N S 310 TRP C C N N 311 TRP O O N N 312 TRP CB C N N 313 TRP CG C Y N 314 TRP CD1 C Y N 315 TRP CD2 C Y N 316 TRP NE1 N Y N 317 TRP CE2 C Y N 318 TRP CE3 C Y N 319 TRP CZ2 C Y N 320 TRP CZ3 C Y N 321 TRP CH2 C Y N 322 TRP OXT O N N 323 TRP H H N N 324 TRP H2 H N N 325 TRP HA H N N 326 TRP HB2 H N N 327 TRP HB3 H N N 328 TRP HD1 H N N 329 TRP HE1 H N N 330 TRP HE3 H N N 331 TRP HZ2 H N N 332 TRP HZ3 H N N 333 TRP HH2 H N N 334 TRP HXT H N N 335 TYR N N N N 336 TYR CA C N S 337 TYR C C N N 338 TYR O O N N 339 TYR CB C N N 340 TYR CG C Y N 341 TYR CD1 C Y N 342 TYR CD2 C Y N 343 TYR CE1 C Y N 344 TYR CE2 C Y N 345 TYR CZ C Y N 346 TYR OH O N N 347 TYR OXT O N N 348 TYR H H N N 349 TYR H2 H N N 350 TYR HA H N N 351 TYR HB2 H N N 352 TYR HB3 H N N 353 TYR HD1 H N N 354 TYR HD2 H N N 355 TYR HE1 H N N 356 TYR HE2 H N N 357 TYR HH H N N 358 TYR HXT H N N 359 VAL N N N N 360 VAL CA C N S 361 VAL C C N N 362 VAL O O N N 363 VAL CB C N N 364 VAL CG1 C N N 365 VAL CG2 C N N 366 VAL OXT O N N 367 VAL H H N N 368 VAL H2 H N N 369 VAL HA H N N 370 VAL HB H N N 371 VAL HG11 H N N 372 VAL HG12 H N N 373 VAL HG13 H N N 374 VAL HG21 H N N 375 VAL HG22 H N N 376 VAL HG23 H N N 377 VAL HXT H N N 378 # 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 A2G O5 C5 sing N N 1 A2G C1 O5 sing N N 2 A2G C1 C2 sing N N 3 A2G C1 H1 sing N N 4 A2G O1 C1 sing N N 5 A2G O1 HO1 sing N N 6 A2G C2 C3 sing N N 7 A2G C2 H2 sing N N 8 A2G N2 C2 sing N N 9 A2G N2 HN2 sing N N 10 A2G C3 C4 sing N N 11 A2G C3 O3 sing N N 12 A2G C3 H3 sing N N 13 A2G O3 HO3 sing N N 14 A2G C4 O4 sing N N 15 A2G C4 H4 sing N N 16 A2G O4 HO4 sing N N 17 A2G C5 C4 sing N N 18 A2G C5 C6 sing N N 19 A2G C5 H5 sing N N 20 A2G C6 O6 sing N N 21 A2G C6 H61 sing N N 22 A2G C7 N2 sing N N 23 A2G O7 C7 doub N N 24 A2G C8 C7 sing N N 25 A2G C8 H81 sing N N 26 A2G C8 H82 sing N N 27 A2G C8 H83 sing N N 28 A2G C6 H62 sing N N 29 A2G O6 HO6 sing N N 30 ALA N CA sing N N 31 ALA N H sing N N 32 ALA N H2 sing N N 33 ALA CA C sing N N 34 ALA CA CB sing N N 35 ALA CA HA sing N N 36 ALA C O doub N N 37 ALA C OXT sing N N 38 ALA CB HB1 sing N N 39 ALA CB HB2 sing N N 40 ALA CB HB3 sing N N 41 ALA OXT HXT sing N N 42 ARG N CA sing N N 43 ARG N H sing N N 44 ARG N H2 sing N N 45 ARG CA C sing N N 46 ARG CA CB sing N N 47 ARG CA HA sing N N 48 ARG C O doub N N 49 ARG C OXT sing N N 50 ARG CB CG sing N N 51 ARG CB HB2 sing N N 52 ARG CB HB3 sing N N 53 ARG CG CD sing N N 54 ARG CG HG2 sing N N 55 ARG CG HG3 sing N N 56 ARG CD NE sing N N 57 ARG CD HD2 sing N N 58 ARG CD HD3 sing N N 59 ARG NE CZ sing N N 60 ARG NE HE sing N N 61 ARG CZ NH1 sing N N 62 ARG CZ NH2 doub N N 63 ARG NH1 HH11 sing N N 64 ARG NH1 HH12 sing N N 65 ARG NH2 HH21 sing N N 66 ARG NH2 HH22 sing N N 67 ARG OXT HXT sing N N 68 ASN N CA sing N N 69 ASN N H sing N N 70 ASN N H2 sing N N 71 ASN CA C sing N N 72 ASN CA CB sing N N 73 ASN CA HA sing N N 74 ASN C O doub N N 75 ASN C OXT sing N N 76 ASN CB CG sing N N 77 ASN CB HB2 sing N N 78 ASN CB HB3 sing N N 79 ASN CG OD1 doub N N 80 ASN CG ND2 sing N N 81 ASN ND2 HD21 sing N N 82 ASN ND2 HD22 sing N N 83 ASN OXT HXT sing N N 84 ASP N CA sing N N 85 ASP N H sing N N 86 ASP N H2 sing N N 87 ASP CA C sing N N 88 ASP CA CB sing N N 89 ASP CA HA sing N N 90 ASP C O doub N N 91 ASP C OXT sing N N 92 ASP CB CG sing N N 93 ASP CB HB2 sing N N 94 ASP CB HB3 sing N N 95 ASP CG OD1 doub N N 96 ASP CG OD2 sing N N 97 ASP OD2 HD2 sing N N 98 ASP OXT HXT sing N N 99 GLN N CA sing N N 100 GLN N H sing N N 101 GLN N H2 sing N N 102 GLN CA C sing N N 103 GLN CA CB sing N N 104 GLN CA HA sing N N 105 GLN C O doub N N 106 GLN C OXT sing N N 107 GLN CB CG sing N N 108 GLN CB HB2 sing N N 109 GLN CB HB3 sing N N 110 GLN CG CD sing N N 111 GLN CG HG2 sing N N 112 GLN CG HG3 sing N N 113 GLN CD OE1 doub N N 114 GLN CD NE2 sing N N 115 GLN NE2 HE21 sing N N 116 GLN NE2 HE22 sing N N 117 GLN OXT HXT sing N N 118 GLU N CA sing N N 119 GLU N H sing N N 120 GLU N H2 sing N N 121 GLU CA C sing N N 122 GLU CA CB sing N N 123 GLU CA HA sing N N 124 GLU C O doub N N 125 GLU C OXT sing N N 126 GLU CB CG sing N N 127 GLU CB HB2 sing N N 128 GLU CB HB3 sing N N 129 GLU CG CD sing N N 130 GLU CG HG2 sing N N 131 GLU CG HG3 sing N N 132 GLU CD OE1 doub N N 133 GLU CD OE2 sing N N 134 GLU OE2 HE2 sing N N 135 GLU OXT HXT sing N N 136 GLY N CA sing N N 137 GLY N H sing N N 138 GLY N H2 sing N N 139 GLY CA C sing N N 140 GLY CA HA2 sing N N 141 GLY CA HA3 sing N N 142 GLY C O doub N N 143 GLY C OXT sing N N 144 GLY OXT HXT sing N N 145 HIS N CA sing N N 146 HIS N H sing N N 147 HIS N H2 sing N N 148 HIS CA C sing N N 149 HIS CA CB sing N N 150 HIS CA HA sing N N 151 HIS C O doub N N 152 HIS C OXT sing N N 153 HIS CB CG sing N N 154 HIS CB HB2 sing N N 155 HIS CB HB3 sing N N 156 HIS CG ND1 sing Y N 157 HIS CG CD2 doub Y N 158 HIS ND1 CE1 doub Y N 159 HIS ND1 HD1 sing N N 160 HIS CD2 NE2 sing Y N 161 HIS CD2 HD2 sing N N 162 HIS CE1 NE2 sing Y N 163 HIS CE1 HE1 sing N N 164 HIS NE2 HE2 sing N N 165 HIS OXT HXT sing N N 166 ILE N CA sing N N 167 ILE N H sing N N 168 ILE N H2 sing N N 169 ILE CA C sing N N 170 ILE CA CB sing N N 171 ILE CA HA sing N N 172 ILE C O doub N N 173 ILE C OXT sing N N 174 ILE CB CG1 sing N N 175 ILE CB CG2 sing N N 176 ILE CB HB sing N N 177 ILE CG1 CD1 sing N N 178 ILE CG1 HG12 sing N N 179 ILE CG1 HG13 sing N N 180 ILE CG2 HG21 sing N N 181 ILE CG2 HG22 sing N N 182 ILE CG2 HG23 sing N N 183 ILE CD1 HD11 sing N N 184 ILE CD1 HD12 sing N N 185 ILE CD1 HD13 sing N N 186 ILE OXT HXT sing N N 187 LEU N CA sing N N 188 LEU N H sing N N 189 LEU N H2 sing N N 190 LEU CA C sing N N 191 LEU CA CB sing N N 192 LEU CA HA sing N N 193 LEU C O doub N N 194 LEU C OXT sing N N 195 LEU CB CG sing N N 196 LEU CB HB2 sing N N 197 LEU CB HB3 sing N N 198 LEU CG CD1 sing N N 199 LEU CG CD2 sing N N 200 LEU CG HG sing N N 201 LEU CD1 HD11 sing N N 202 LEU CD1 HD12 sing N N 203 LEU CD1 HD13 sing N N 204 LEU CD2 HD21 sing N N 205 LEU CD2 HD22 sing N N 206 LEU CD2 HD23 sing N N 207 LEU OXT HXT sing N N 208 MET N CA sing N N 209 MET N H sing N N 210 MET N H2 sing N N 211 MET CA C sing N N 212 MET CA CB sing N N 213 MET CA HA sing N N 214 MET C O doub N N 215 MET C OXT sing N N 216 MET CB CG sing N N 217 MET CB HB2 sing N N 218 MET CB HB3 sing N N 219 MET CG SD sing N N 220 MET CG HG2 sing N N 221 MET CG HG3 sing N N 222 MET SD CE sing N N 223 MET CE HE1 sing N N 224 MET CE HE2 sing N N 225 MET CE HE3 sing N N 226 MET OXT HXT sing N N 227 PHE N CA sing N N 228 PHE N H sing N N 229 PHE N H2 sing N N 230 PHE CA C sing N N 231 PHE CA CB sing N N 232 PHE CA HA sing N N 233 PHE C O doub N N 234 PHE C OXT sing N N 235 PHE CB CG sing N N 236 PHE CB HB2 sing N N 237 PHE CB HB3 sing N N 238 PHE CG CD1 doub Y N 239 PHE CG CD2 sing Y N 240 PHE CD1 CE1 sing Y N 241 PHE CD1 HD1 sing N N 242 PHE CD2 CE2 doub Y N 243 PHE CD2 HD2 sing N N 244 PHE CE1 CZ doub Y N 245 PHE CE1 HE1 sing N N 246 PHE CE2 CZ sing Y N 247 PHE CE2 HE2 sing N N 248 PHE CZ HZ sing N N 249 PHE OXT HXT sing N N 250 PRO N CA sing N N 251 PRO N CD sing N N 252 PRO N H sing N N 253 PRO CA C sing N N 254 PRO CA CB sing N N 255 PRO CA HA sing N N 256 PRO C O doub N N 257 PRO C OXT sing N N 258 PRO CB CG sing N N 259 PRO CB HB2 sing N N 260 PRO CB HB3 sing N N 261 PRO CG CD sing N N 262 PRO CG HG2 sing N N 263 PRO CG HG3 sing N N 264 PRO CD HD2 sing N N 265 PRO CD HD3 sing N N 266 PRO OXT HXT sing N N 267 SER N CA sing N N 268 SER N H sing N N 269 SER N H2 sing N N 270 SER CA C sing N N 271 SER CA CB sing N N 272 SER CA HA sing N N 273 SER C O doub N N 274 SER C OXT sing N N 275 SER CB OG sing N N 276 SER CB HB2 sing N N 277 SER CB HB3 sing N N 278 SER OG HG sing N N 279 SER OXT HXT sing N N 280 THR N CA sing N N 281 THR N H sing N N 282 THR N H2 sing N N 283 THR CA C sing N N 284 THR CA CB sing N N 285 THR CA HA sing N N 286 THR C O doub N N 287 THR C OXT sing N N 288 THR CB OG1 sing N N 289 THR CB CG2 sing N N 290 THR CB HB sing N N 291 THR OG1 HG1 sing N N 292 THR CG2 HG21 sing N N 293 THR CG2 HG22 sing N N 294 THR CG2 HG23 sing N N 295 THR OXT HXT sing N N 296 TRP N CA sing N N 297 TRP N H sing N N 298 TRP N H2 sing N N 299 TRP CA C sing N N 300 TRP CA CB sing N N 301 TRP CA HA sing N N 302 TRP C O doub N N 303 TRP C OXT sing N N 304 TRP CB CG sing N N 305 TRP CB HB2 sing N N 306 TRP CB HB3 sing N N 307 TRP CG CD1 doub Y N 308 TRP CG CD2 sing Y N 309 TRP CD1 NE1 sing Y N 310 TRP CD1 HD1 sing N N 311 TRP CD2 CE2 doub Y N 312 TRP CD2 CE3 sing Y N 313 TRP NE1 CE2 sing Y N 314 TRP NE1 HE1 sing N N 315 TRP CE2 CZ2 sing Y N 316 TRP CE3 CZ3 doub Y N 317 TRP CE3 HE3 sing N N 318 TRP CZ2 CH2 doub Y N 319 TRP CZ2 HZ2 sing N N 320 TRP CZ3 CH2 sing Y N 321 TRP CZ3 HZ3 sing N N 322 TRP CH2 HH2 sing N N 323 TRP OXT HXT sing N N 324 TYR N CA sing N N 325 TYR N H sing N N 326 TYR N H2 sing N N 327 TYR CA C sing N N 328 TYR CA CB sing N N 329 TYR CA HA sing N N 330 TYR C O doub N N 331 TYR C OXT sing N N 332 TYR CB CG sing N N 333 TYR CB HB2 sing N N 334 TYR CB HB3 sing N N 335 TYR CG CD1 doub Y N 336 TYR CG CD2 sing Y N 337 TYR CD1 CE1 sing Y N 338 TYR CD1 HD1 sing N N 339 TYR CD2 CE2 doub Y N 340 TYR CD2 HD2 sing N N 341 TYR CE1 CZ doub Y N 342 TYR CE1 HE1 sing N N 343 TYR CE2 CZ sing Y N 344 TYR CE2 HE2 sing N N 345 TYR CZ OH sing N N 346 TYR OH HH sing N N 347 TYR OXT HXT sing N N 348 VAL N CA sing N N 349 VAL N H sing N N 350 VAL N H2 sing N N 351 VAL CA C sing N N 352 VAL CA CB sing N N 353 VAL CA HA sing N N 354 VAL C O doub N N 355 VAL C OXT sing N N 356 VAL CB CG1 sing N N 357 VAL CB CG2 sing N N 358 VAL CB HB sing N N 359 VAL CG1 HG11 sing N N 360 VAL CG1 HG12 sing N N 361 VAL CG1 HG13 sing N N 362 VAL CG2 HG21 sing N N 363 VAL CG2 HG22 sing N N 364 VAL CG2 HG23 sing N N 365 VAL OXT HXT sing N N 366 # _em_admin.current_status REL _em_admin.deposition_date 2024-11-14 _em_admin.deposition_site PDBJ _em_admin.entry_id 9KL3 _em_admin.last_update 2025-12-31 _em_admin.map_release_date 2025-11-19 _em_admin.title 'CryoEM structure of Pleurocybella porrigens lectin (PPL) in complex with GalNAc' # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.experimental_flag YES _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.units MEGADALTONS _em_entity_assembly_molwt.value 0.0856 # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 1 _em_entity_assembly_naturalsource.ncbi_tax_id 71910 _em_entity_assembly_naturalsource.organism 'Pleurocybella porrigens' _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_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.id 1 _em_entity_assembly_recombinant.ncbi_tax_id 562 _em_entity_assembly_recombinant.organism 'Escherichia coli' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time 4.8 _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 47.41 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K2 SUMMIT (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 1542 # _em_particle_selection.details ? _em_particle_selection.id 1 _em_particle_selection.image_processing_id 1 _em_particle_selection.method ? _em_particle_selection.num_particles_selected 150096 _em_particle_selection.reference_model ? # 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 'PARTICLE SELECTION' ? 1 1 ? ? Topaz ? 'IMAGE ACQUISITION' ? 2 ? ? 1 SerialEM ? MASKING ? 3 ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? cryoSPARC ? 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? 'MODEL FITTING' ? 7 ? 1 ? Coot ? 'MODEL FITTING' ? 8 ? 1 ? 'UCSF ChimeraX' ? OTHER ? 9 ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? cryoSPARC ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? cryoSPARC ? CLASSIFICATION ? 12 1 ? ? cryoSPARC ? RECONSTRUCTION ? 13 1 ? ? cryoSPARC ? 'VOLUME SELECTION' ? 14 1 1 1 ? ? 'SERIES ALIGNMENT' ? 15 1 1 1 ? ? 'MOLECULAR REPLACEMENT' ? 16 1 1 1 ? ? 'LATTICE DISTORTION CORRECTION' ? 17 1 1 1 ? ? 'SYMMETRY DETERMINATION' ? 18 1 1 1 ? ? 'CRYSTALLOGRAPHY MERGING' ? 19 1 1 1 ? ? 'MODEL REFINEMENT' ? 20 ? 1 ? PHENIX ? # _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 # _pdbx_audit_support.funding_organization 'Other private' _pdbx_audit_support.country ? _pdbx_audit_support.grant_number Y-2023-2-046 _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 9KL3 _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] 1.000000 _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] 1.000000 _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] 1.000000 _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_ #