data_5RVL # _entry.id 5RVL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.358 _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 5RVL pdb_00005rvl 10.2210/pdb5rvl/pdb WWPDB D_1001403726 ? ? # _pdbx_database_status.entry_id 5RVL _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.recvd_initial_deposition_date 2020-10-02 _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Correy, G.C.' 1 ? 'Young, I.D.' 2 ? 'Thompson, M.C.' 3 ? 'Fraser, J.S.' 4 ? # _citation.id primary _citation.title 'Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.' _citation.journal_abbrev 'Sci Adv' _citation.journal_volume 7 _citation.page_first ? _citation.page_last ? _citation.year 2021 _citation.pdbx_database_id_PubMed 33853786 _citation.pdbx_database_id_DOI 10.1126/sciadv.abf8711 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 2375-2548 _citation.journal_id_CSD ? _citation.book_publisher ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.identifier_ORCID _citation_author.ordinal primary 'Schuller, M.' 0000-0002-1551-0359 1 primary 'Correy, G.J.' 0000-0001-5155-7325 2 primary 'Gahbauer, S.' 0000-0002-3115-9757 3 primary 'Fearon, D.' 0000-0003-3529-7863 4 primary 'Wu, T.' 0000-0001-6988-1414 5 primary 'Diaz, R.E.' 0000-0002-1172-9919 6 primary 'Young, I.D.' 0000-0003-4713-9504 7 primary 'Carvalho Martins, L.' 0000-0002-7747-6782 8 primary 'Smith, D.H.' 0000-0002-5136-4491 9 primary 'Schulze-Gahmen, U.' 0000-0003-3919-4474 10 primary 'Owens, T.W.' 0000-0001-7423-4879 11 primary 'Deshpande, I.' 0000-0002-8276-9635 12 primary 'Merz, G.E.' 0000-0003-0842-4935 13 primary 'Thwin, A.C.' 0000-0002-1423-8189 14 primary 'Biel, J.T.' 0000-0002-0935-8362 15 primary 'Peters, J.K.' 0000-0003-3541-7431 16 primary 'Moritz, M.' 0000-0003-3811-5623 17 primary 'Herrera, N.' 0000-0003-4157-9429 18 primary 'Kratochvil, H.T.' 0000-0001-8039-6823 19 primary 'Aimon, A.' 0000-0002-9135-129X 20 primary 'Bennett, J.M.' 0000-0003-1396-8400 21 primary 'Brandao Neto, J.' 0000-0001-6015-320X 22 primary 'Cohen, A.E.' 0000-0003-2414-9427 23 primary 'Dias, A.' 0000-0003-3609-7003 24 primary 'Douangamath, A.' ? 25 primary 'Dunnett, L.' 0000-0001-6710-6959 26 primary 'Fedorov, O.' 0000-0002-8662-7300 27 primary 'Ferla, M.P.' ? 28 primary 'Fuchs, M.R.' 0000-0001-9784-0927 29 primary 'Gorrie-Stone, T.J.' 0000-0002-1817-1495 30 primary 'Holton, J.M.' 0000-0002-0596-0137 31 primary 'Johnson, M.G.' 0000-0001-9213-0598 32 primary 'Krojer, T.' 0000-0003-0661-0814 33 primary 'Meigs, G.' 0000-0002-8530-661X 34 primary 'Powell, A.J.' 0000-0002-0462-2240 35 primary 'Rack, J.G.M.' 0000-0001-8341-6439 36 primary 'Rangel, V.L.' 0000-0002-7580-3452 37 primary 'Russi, S.' ? 38 primary 'Skyner, R.E.' 0000-0003-3614-6661 39 primary 'Smith, C.A.' 0000-0002-1885-1511 40 primary 'Soares, A.S.' 0000-0002-6565-8503 41 primary 'Wierman, J.L.' 0000-0002-5206-9662 42 primary 'Zhu, K.' ? 43 primary ;O'Brien, P. ; 0000-0002-9966-1962 44 primary 'Jura, N.' 0000-0001-5129-641X 45 primary 'Ashworth, A.' 0000-0003-1446-7878 46 primary 'Irwin, J.J.' 0000-0002-1195-6417 47 primary 'Thompson, M.C.' 0000-0002-6099-2027 48 primary 'Gestwicki, J.E.' ? 49 primary 'von Delft, F.' 0000-0003-0378-0017 50 primary 'Shoichet, B.K.' 0000-0002-6098-7367 51 primary 'Fraser, J.S.' 0000-0002-5080-2859 52 primary 'Ahel, I.' 0000-0002-9446-3756 53 # _cell.entry_id 5RVL _cell.length_a 132.480 _cell.length_b 29.900 _cell.length_c 37.220 _cell.angle_alpha 90.000 _cell.angle_beta 98.790 _cell.angle_gamma 90.000 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5RVL _symmetry.Int_Tables_number 5 _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? # 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 'Non-structural protein 3' 18548.027 1 '3.4.19.121, 3.4.22.-' ? macrodomain 'HIS6 purification tag (MHHHHHHENLYFQ) cleaved with TEV protease' 2 non-polymer syn 4-METHYLPYRIDIN-2-AMINE 108.141 1 ? ? ? ? 3 water nat water 18.015 154 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO' # _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 ;SNAGEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKV GGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFD KNLYDKLVSSFLE ; _entity_poly.pdbx_seq_one_letter_code_can ;SNAGEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKV GGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFD KNLYDKLVSSFLE ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 SER n 1 2 ASN n 1 3 ALA n 1 4 GLY n 1 5 GLU n 1 6 VAL n 1 7 ASN n 1 8 SER n 1 9 PHE n 1 10 SER n 1 11 GLY n 1 12 TYR n 1 13 LEU n 1 14 LYS n 1 15 LEU n 1 16 THR n 1 17 ASP n 1 18 ASN n 1 19 VAL n 1 20 TYR n 1 21 ILE n 1 22 LYS n 1 23 ASN n 1 24 ALA n 1 25 ASP n 1 26 ILE n 1 27 VAL n 1 28 GLU n 1 29 GLU n 1 30 ALA n 1 31 LYS n 1 32 LYS n 1 33 VAL n 1 34 LYS n 1 35 PRO n 1 36 THR n 1 37 VAL n 1 38 VAL n 1 39 VAL n 1 40 ASN n 1 41 ALA n 1 42 ALA n 1 43 ASN n 1 44 VAL n 1 45 TYR n 1 46 LEU n 1 47 LYS n 1 48 HIS n 1 49 GLY n 1 50 GLY n 1 51 GLY n 1 52 VAL n 1 53 ALA n 1 54 GLY n 1 55 ALA n 1 56 LEU n 1 57 ASN n 1 58 LYS n 1 59 ALA n 1 60 THR n 1 61 ASN n 1 62 ASN n 1 63 ALA n 1 64 MET n 1 65 GLN n 1 66 VAL n 1 67 GLU n 1 68 SER n 1 69 ASP n 1 70 ASP n 1 71 TYR n 1 72 ILE n 1 73 ALA n 1 74 THR n 1 75 ASN n 1 76 GLY n 1 77 PRO n 1 78 LEU n 1 79 LYS n 1 80 VAL n 1 81 GLY n 1 82 GLY n 1 83 SER n 1 84 CYS n 1 85 VAL n 1 86 LEU n 1 87 SER n 1 88 GLY n 1 89 HIS n 1 90 ASN n 1 91 LEU n 1 92 ALA n 1 93 LYS n 1 94 HIS n 1 95 CYS n 1 96 LEU n 1 97 HIS n 1 98 VAL n 1 99 VAL n 1 100 GLY n 1 101 PRO n 1 102 ASN n 1 103 VAL n 1 104 ASN n 1 105 LYS n 1 106 GLY n 1 107 GLU n 1 108 ASP n 1 109 ILE n 1 110 GLN n 1 111 LEU n 1 112 LEU n 1 113 LYS n 1 114 SER n 1 115 ALA n 1 116 TYR n 1 117 GLU n 1 118 ASN n 1 119 PHE n 1 120 ASN n 1 121 GLN n 1 122 HIS n 1 123 GLU n 1 124 VAL n 1 125 LEU n 1 126 LEU n 1 127 ALA n 1 128 PRO n 1 129 LEU n 1 130 LEU n 1 131 SER n 1 132 ALA n 1 133 GLY n 1 134 ILE n 1 135 PHE n 1 136 GLY n 1 137 ALA n 1 138 ASP n 1 139 PRO n 1 140 ILE n 1 141 HIS n 1 142 SER n 1 143 LEU n 1 144 ARG n 1 145 VAL n 1 146 CYS n 1 147 VAL n 1 148 ASP n 1 149 THR n 1 150 VAL n 1 151 ARG n 1 152 THR n 1 153 ASN n 1 154 VAL n 1 155 TYR n 1 156 LEU n 1 157 ALA n 1 158 VAL n 1 159 PHE n 1 160 ASP n 1 161 LYS n 1 162 ASN n 1 163 LEU n 1 164 TYR n 1 165 ASP n 1 166 LYS n 1 167 LEU n 1 168 VAL n 1 169 SER n 1 170 SER n 1 171 PHE n 1 172 LEU n 1 173 GLU 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 173 _entity_src_gen.gene_src_common_name 2019-nCoV _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'rep, 1a-1b' _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 'Severe acute respiratory syndrome coronavirus 2' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 2697049 _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 BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _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 plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name 'pET22b(+)' _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code R1AB_SARS2 _struct_ref.pdbx_db_accession P0DTD1 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;EVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSC VLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLY DKLVSSFLE ; _struct_ref.pdbx_align_begin 1024 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5RVL _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 5 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 173 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P0DTD1 _struct_ref_seq.db_align_beg 1024 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 1192 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2 _struct_ref_seq.pdbx_auth_seq_align_end 170 # 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 5RVL SER A 1 ? UNP P0DTD1 ? ? 'expression tag' -2 1 1 5RVL ASN A 2 ? UNP P0DTD1 ? ? 'expression tag' -1 2 1 5RVL ALA A 3 ? UNP P0DTD1 ? ? 'expression tag' 0 3 1 5RVL GLY A 4 ? UNP P0DTD1 ? ? 'expression tag' 1 4 # 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 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 BVF non-polymer . 4-METHYLPYRIDIN-2-AMINE 2-AMINO-4-PICOLINE 'C6 H8 N2' 108.141 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 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 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 _exptl.entry_id 5RVL # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.96 _exptl_crystal.density_percent_sol 37.37 _exptl_crystal.density_meas ? _exptl_crystal.description ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH 8.5 _exptl_crystal_grow.temp 293 _exptl_crystal_grow.pdbx_details '100 mM TRIS, 50 mM sodium acetate, 28% PEG 4000' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp_details ? # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.pdbx_serial_crystal_experiment ? # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS3 6M' _diffrn_detector.pdbx_collection_date 2020-05-30 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_scattering_type x-ray _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.033 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALS BEAMLINE 8.3.1' _diffrn_source.pdbx_wavelength_list 1.033 _diffrn_source.pdbx_synchrotron_site ALS _diffrn_source.pdbx_synchrotron_beamline 8.3.1 _diffrn_source.pdbx_wavelength ? # _reflns.entry_id 5RVL _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 36.780 _reflns.d_resolution_high 1.360 _reflns.number_obs 30219 _reflns.number_all ? _reflns.percent_possible_obs 96.400 _reflns.pdbx_Rmerge_I_obs 0.067 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 10.180 _reflns.B_iso_Wilson_estimate 23.241 _reflns.pdbx_redundancy 3.328 _reflns.pdbx_Rrim_I_all 0.080 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_CC_half 0.999 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_number_measured_all 100569 _reflns.pdbx_scaling_rejects 19 _reflns.pdbx_chi_squared 1.010 _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.details ? _reflns.pdbx_CC_star ? # loop_ _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.pdbx_rejects _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.meanI_over_sigI_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star 1 1 1.360 1.400 7314 ? 2147 ? 1.596 0.810 ? ? 3.407 ? ? 2262 ? ? ? ? ? 94.900 1.894 ? 0.352 ? 1 2 1.400 1.430 7216 ? 2135 ? 1.320 0.970 ? ? 3.380 ? ? 2256 ? ? ? ? ? 94.600 1.570 ? 0.402 ? 1 3 1.430 1.480 6792 ? 2057 ? 1.045 1.250 ? ? 3.302 ? ? 2171 ? ? ? ? ? 94.700 1.251 ? 0.455 ? 1 4 1.480 1.520 6416 ? 2031 ? 0.906 1.400 ? ? 3.159 ? ? 2115 ? ? ? ? ? 96.000 1.090 ? 0.552 ? 1 5 1.520 1.570 6607 ? 1963 ? 0.655 2.030 ? ? 3.366 ? ? 2077 ? ? ? ? ? 94.500 0.777 ? 0.760 ? 1 6 1.570 1.630 6655 ? 1913 ? 0.498 2.750 ? ? 3.479 ? ? 1962 ? ? ? ? ? 97.500 0.588 ? 0.814 ? 1 7 1.630 1.690 6437 ? 1868 ? 0.383 3.540 ? ? 3.446 ? ? 1935 ? ? ? ? ? 96.500 0.453 ? 0.859 ? 1 8 1.690 1.760 6071 ? 1778 ? 0.319 4.230 ? ? 3.415 ? ? 1864 ? ? ? ? ? 95.400 0.380 ? 0.897 ? 1 9 1.760 1.830 5742 ? 1751 ? 0.233 5.620 ? ? 3.279 ? ? 1773 ? ? ? ? ? 98.800 0.279 ? 0.936 ? 1 10 1.830 1.920 5104 ? 1632 ? 0.165 7.500 ? ? 3.127 ? ? 1685 ? ? ? ? ? 96.900 0.198 ? 0.966 ? 1 11 1.920 2.030 5480 ? 1561 ? 0.117 10.780 ? ? 3.511 ? ? 1613 ? ? ? ? ? 96.800 0.138 ? 0.986 ? 1 12 2.030 2.150 5153 ? 1504 ? 0.080 14.730 ? ? 3.426 ? ? 1555 ? ? ? ? ? 96.700 0.096 ? 0.993 ? 1 13 2.150 2.300 4742 ? 1412 ? 0.064 17.860 ? ? 3.358 ? ? 1447 ? ? ? ? ? 97.600 0.076 ? 0.995 ? 1 14 2.300 2.480 4313 ? 1318 ? 0.053 19.790 ? ? 3.272 ? ? 1351 ? ? ? ? ? 97.600 0.064 ? 0.996 ? 1 15 2.480 2.720 3562 ? 1194 ? 0.044 22.080 ? ? 2.983 ? ? 1238 ? ? ? ? ? 96.400 0.054 ? 0.997 ? 1 16 2.720 3.040 3760 ? 1106 ? 0.036 28.190 ? ? 3.400 ? ? 1127 ? ? ? ? ? 98.100 0.043 ? 0.998 ? 1 17 3.040 3.510 3259 ? 971 ? 0.029 34.520 ? ? 3.356 ? ? 998 ? ? ? ? ? 97.300 0.035 ? 0.998 ? 1 18 3.510 4.300 2648 ? 832 ? 0.024 37.360 ? ? 3.183 ? ? 868 ? ? ? ? ? 95.900 0.029 ? 0.999 ? 1 19 4.300 6.080 2020 ? 667 ? 0.022 37.530 ? ? 3.028 ? ? 674 ? ? ? ? ? 99.000 0.026 ? 0.999 ? 1 20 6.080 36.780 1278 ? 379 ? 0.019 40.780 ? ? 3.372 ? ? 386 ? ? ? ? ? 98.200 0.023 ? 0.999 ? # _refine.entry_id 5RVL _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_d_res_high 1.3600 _refine.ls_d_res_low 36.7800 _refine.pdbx_ls_sigma_F 1.340 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 96.3600 _refine.ls_number_reflns_obs 30206 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.ls_matrix_type ? _refine.pdbx_R_Free_selection_details ? _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1658 _refine.ls_R_factor_R_work 0.1643 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.1948 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.7900 _refine.ls_number_reflns_R_free 1446 _refine.ls_number_reflns_R_work 28760 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 24.3643 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _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.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _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 ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.1500 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 79.390 _refine.B_iso_min 10.800 _refine.pdbx_overall_phase_error 22.9600 _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_R_factor_R_free_error_details ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.3600 _refine_hist.d_res_low 36.7800 _refine_hist.pdbx_number_atoms_ligand 16 _refine_hist.number_atoms_solvent 154 _refine_hist.number_atoms_total 1443 _refine_hist.pdbx_number_residues_total 168 _refine_hist.pdbx_B_iso_mean_ligand 58.47 _refine_hist.pdbx_B_iso_mean_solvent 33.56 _refine_hist.pdbx_number_atoms_protein 1273 _refine_hist.pdbx_number_atoms_nucleic_acid 0 # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.pdbx_refine_id _refine_ls_shell.R_factor_obs 1.3600 1.4100 10 94.0000 2803 . 0.2833 0.3431 . 127 0.0000 2930 . 'X-RAY DIFFRACTION' . 1.4100 1.4700 10 95.0000 2770 . 0.2648 0.3337 . 148 0.0000 2918 . 'X-RAY DIFFRACTION' . 1.4700 1.5300 10 95.0000 2805 . 0.2496 0.3180 . 145 0.0000 2950 . 'X-RAY DIFFRACTION' . 1.5300 1.6100 10 96.0000 2906 . 0.1994 0.2391 . 125 0.0000 3031 . 'X-RAY DIFFRACTION' . 1.6100 1.7100 10 97.0000 2858 . 0.1718 0.2485 . 148 0.0000 3006 . 'X-RAY DIFFRACTION' . 1.7100 1.8500 10 97.0000 2873 . 0.1554 0.2470 . 144 0.0000 3017 . 'X-RAY DIFFRACTION' . 1.8500 2.0300 10 97.0000 2881 . 0.1409 0.1717 . 148 0.0000 3029 . 'X-RAY DIFFRACTION' . 2.0300 2.3300 10 97.0000 2919 . 0.1372 0.1817 . 158 0.0000 3077 . 'X-RAY DIFFRACTION' . 2.3300 2.9300 10 97.0000 2923 . 0.1522 0.1714 . 145 0.0000 3068 . 'X-RAY DIFFRACTION' . 2.9300 36.7800 10 97.0000 3022 . 0.1589 0.1674 . 158 0.0000 3180 . 'X-RAY DIFFRACTION' . # _struct.entry_id 5RVL _struct.title 'PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000149580' _struct.pdbx_CASP_flag ? _struct.pdbx_model_details ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 5RVL _struct_keywords.pdbx_keywords 'VIRAL PROTEIN' _struct_keywords.text 'Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL 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 ? C N N 3 ? # 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 ASP A 25 ? LYS A 34 ? ASP A 22 LYS A 31 1 ? 10 HELX_P HELX_P2 AA2 GLY A 50 ? THR A 60 ? GLY A 47 THR A 57 1 ? 11 HELX_P HELX_P3 AA3 ASN A 62 ? GLY A 76 ? ASN A 59 GLY A 73 1 ? 15 HELX_P HELX_P4 AA4 ASN A 102 ? GLY A 106 ? ASN A 99 GLY A 103 5 ? 5 HELX_P HELX_P5 AA5 GLN A 110 ? ASN A 118 ? GLN A 107 ASN A 115 1 ? 9 HELX_P HELX_P6 AA6 PHE A 119 ? HIS A 122 ? PHE A 116 HIS A 119 5 ? 4 HELX_P HELX_P7 AA7 ALA A 132 ? GLY A 136 ? ALA A 129 GLY A 133 5 ? 5 HELX_P HELX_P8 AA8 ASP A 138 ? VAL A 150 ? ASP A 135 VAL A 147 1 ? 13 HELX_P HELX_P9 AA9 ASP A 160 ? GLU A 173 ? ASP A 157 GLU A 170 1 ? 14 # _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 ? 4 ? AA2 ? 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 ? parallel AA1 3 4 ? parallel AA2 1 2 ? parallel AA2 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 LEU A 13 ? THR A 16 ? LEU A 10 THR A 13 AA1 2 VAL A 19 ? ASN A 23 ? VAL A 16 ASN A 20 AA1 3 ASN A 153 ? VAL A 158 ? ASN A 150 VAL A 155 AA1 4 VAL A 124 ? ALA A 127 ? VAL A 121 ALA A 124 AA2 1 VAL A 37 ? ALA A 41 ? VAL A 34 ALA A 38 AA2 2 HIS A 94 ? VAL A 98 ? HIS A 91 VAL A 95 AA2 3 SER A 83 ? SER A 87 ? SER A 80 SER A 84 # 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 LEU A 13 ? N LEU A 10 O ILE A 21 ? O ILE A 18 AA1 2 3 N LYS A 22 ? N LYS A 19 O VAL A 158 ? O VAL A 155 AA1 3 4 O TYR A 155 ? O TYR A 152 N LEU A 125 ? N LEU A 122 AA2 1 2 N ASN A 40 ? N ASN A 37 O VAL A 98 ? O VAL A 95 AA2 2 3 O HIS A 97 ? O HIS A 94 N CYS A 84 ? N CYS A 81 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id BVF _struct_site.pdbx_auth_seq_id 201 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 5 _struct_site.details 'binding site for residue BVF A 201' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 5 ASP A 25 ? ASP A 22 . ? 1_555 ? 2 AC1 5 ILE A 26 ? ILE A 23 . ? 1_555 ? 3 AC1 5 VAL A 52 ? VAL A 49 . ? 1_555 ? 4 AC1 5 GLU A 123 ? GLU A 120 . ? 1_565 ? 5 AC1 5 HOH C . ? HOH A 326 . ? 1_555 ? # _atom_sites.entry_id 5RVL _atom_sites.fract_transf_matrix[1][1] 0.007548 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.001167 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.033445 _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] 0.027187 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C H N O S # 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 SER 1 -2 ? ? ? A . n A 1 2 ASN 2 -1 ? ? ? A . n A 1 3 ALA 3 0 ? ? ? A . n A 1 4 GLY 4 1 ? ? ? A . n A 1 5 GLU 5 2 ? ? ? A . n A 1 6 VAL 6 3 3 VAL VAL A . n A 1 7 ASN 7 4 4 ASN ASN A . n A 1 8 SER 8 5 5 SER SER A . n A 1 9 PHE 9 6 6 PHE PHE A . n A 1 10 SER 10 7 7 SER SER A . n A 1 11 GLY 11 8 8 GLY GLY A . n A 1 12 TYR 12 9 9 TYR TYR A . n A 1 13 LEU 13 10 10 LEU LEU A . n A 1 14 LYS 14 11 11 LYS LYS A . n A 1 15 LEU 15 12 12 LEU LEU A . n A 1 16 THR 16 13 13 THR THR A . n A 1 17 ASP 17 14 14 ASP ASP A . n A 1 18 ASN 18 15 15 ASN ASN A . n A 1 19 VAL 19 16 16 VAL VAL A . n A 1 20 TYR 20 17 17 TYR TYR A . n A 1 21 ILE 21 18 18 ILE ILE A . n A 1 22 LYS 22 19 19 LYS LYS A . n A 1 23 ASN 23 20 20 ASN ASN A . n A 1 24 ALA 24 21 21 ALA ALA A . n A 1 25 ASP 25 22 22 ASP ASP A . n A 1 26 ILE 26 23 23 ILE ILE A . n A 1 27 VAL 27 24 24 VAL VAL A . n A 1 28 GLU 28 25 25 GLU GLU A . n A 1 29 GLU 29 26 26 GLU GLU A . n A 1 30 ALA 30 27 27 ALA ALA A . n A 1 31 LYS 31 28 28 LYS LYS A . n A 1 32 LYS 32 29 29 LYS LYS A . n A 1 33 VAL 33 30 30 VAL VAL A . n A 1 34 LYS 34 31 31 LYS LYS A . n A 1 35 PRO 35 32 32 PRO PRO A . n A 1 36 THR 36 33 33 THR THR A . n A 1 37 VAL 37 34 34 VAL VAL A . n A 1 38 VAL 38 35 35 VAL VAL A . n A 1 39 VAL 39 36 36 VAL VAL A . n A 1 40 ASN 40 37 37 ASN ASN A . n A 1 41 ALA 41 38 38 ALA ALA A . n A 1 42 ALA 42 39 39 ALA ALA A . n A 1 43 ASN 43 40 40 ASN ASN A . n A 1 44 VAL 44 41 41 VAL VAL A . n A 1 45 TYR 45 42 42 TYR TYR A . n A 1 46 LEU 46 43 43 LEU LEU A . n A 1 47 LYS 47 44 44 LYS LYS A . n A 1 48 HIS 48 45 45 HIS HIS A . n A 1 49 GLY 49 46 46 GLY GLY A . n A 1 50 GLY 50 47 47 GLY GLY A . n A 1 51 GLY 51 48 48 GLY GLY A . n A 1 52 VAL 52 49 49 VAL VAL A . n A 1 53 ALA 53 50 50 ALA ALA A . n A 1 54 GLY 54 51 51 GLY GLY A . n A 1 55 ALA 55 52 52 ALA ALA A . n A 1 56 LEU 56 53 53 LEU LEU A . n A 1 57 ASN 57 54 54 ASN ASN A . n A 1 58 LYS 58 55 55 LYS LYS A . n A 1 59 ALA 59 56 56 ALA ALA A . n A 1 60 THR 60 57 57 THR THR A . n A 1 61 ASN 61 58 58 ASN ASN A . n A 1 62 ASN 62 59 59 ASN ASN A . n A 1 63 ALA 63 60 60 ALA ALA A . n A 1 64 MET 64 61 61 MET MET A . n A 1 65 GLN 65 62 62 GLN GLN A . n A 1 66 VAL 66 63 63 VAL VAL A . n A 1 67 GLU 67 64 64 GLU GLU A . n A 1 68 SER 68 65 65 SER SER A . n A 1 69 ASP 69 66 66 ASP ASP A . n A 1 70 ASP 70 67 67 ASP ASP A . n A 1 71 TYR 71 68 68 TYR TYR A . n A 1 72 ILE 72 69 69 ILE ILE A . n A 1 73 ALA 73 70 70 ALA ALA A . n A 1 74 THR 74 71 71 THR THR A . n A 1 75 ASN 75 72 72 ASN ASN A . n A 1 76 GLY 76 73 73 GLY GLY A . n A 1 77 PRO 77 74 74 PRO PRO A . n A 1 78 LEU 78 75 75 LEU LEU A . n A 1 79 LYS 79 76 76 LYS LYS A . n A 1 80 VAL 80 77 77 VAL VAL A . n A 1 81 GLY 81 78 78 GLY GLY A . n A 1 82 GLY 82 79 79 GLY GLY A . n A 1 83 SER 83 80 80 SER SER A . n A 1 84 CYS 84 81 81 CYS CYS A . n A 1 85 VAL 85 82 82 VAL VAL A . n A 1 86 LEU 86 83 83 LEU LEU A . n A 1 87 SER 87 84 84 SER SER A . n A 1 88 GLY 88 85 85 GLY GLY A . n A 1 89 HIS 89 86 86 HIS HIS A . n A 1 90 ASN 90 87 87 ASN ASN A . n A 1 91 LEU 91 88 88 LEU LEU A . n A 1 92 ALA 92 89 89 ALA ALA A . n A 1 93 LYS 93 90 90 LYS LYS A . n A 1 94 HIS 94 91 91 HIS HIS A . n A 1 95 CYS 95 92 92 CYS CYS A . n A 1 96 LEU 96 93 93 LEU LEU A . n A 1 97 HIS 97 94 94 HIS HIS A . n A 1 98 VAL 98 95 95 VAL VAL A . n A 1 99 VAL 99 96 96 VAL VAL A . n A 1 100 GLY 100 97 97 GLY GLY A . n A 1 101 PRO 101 98 98 PRO PRO A . n A 1 102 ASN 102 99 99 ASN ASN A . n A 1 103 VAL 103 100 100 VAL VAL A . n A 1 104 ASN 104 101 101 ASN ASN A . n A 1 105 LYS 105 102 102 LYS LYS A . n A 1 106 GLY 106 103 103 GLY GLY A . n A 1 107 GLU 107 104 104 GLU GLU A . n A 1 108 ASP 108 105 105 ASP ASP A . n A 1 109 ILE 109 106 106 ILE ILE A . n A 1 110 GLN 110 107 107 GLN GLN A . n A 1 111 LEU 111 108 108 LEU LEU A . n A 1 112 LEU 112 109 109 LEU LEU A . n A 1 113 LYS 113 110 110 LYS LYS A . n A 1 114 SER 114 111 111 SER SER A . n A 1 115 ALA 115 112 112 ALA ALA A . n A 1 116 TYR 116 113 113 TYR TYR A . n A 1 117 GLU 117 114 114 GLU GLU A . n A 1 118 ASN 118 115 115 ASN ASN A . n A 1 119 PHE 119 116 116 PHE PHE A . n A 1 120 ASN 120 117 117 ASN ASN A . n A 1 121 GLN 121 118 118 GLN GLN A . n A 1 122 HIS 122 119 119 HIS HIS A . n A 1 123 GLU 123 120 120 GLU GLU A . n A 1 124 VAL 124 121 121 VAL VAL A . n A 1 125 LEU 125 122 122 LEU LEU A . n A 1 126 LEU 126 123 123 LEU LEU A . n A 1 127 ALA 127 124 124 ALA ALA A . n A 1 128 PRO 128 125 125 PRO PRO A . n A 1 129 LEU 129 126 126 LEU LEU A . n A 1 130 LEU 130 127 127 LEU LEU A . n A 1 131 SER 131 128 128 SER SER A . n A 1 132 ALA 132 129 129 ALA ALA A . n A 1 133 GLY 133 130 130 GLY GLY A . n A 1 134 ILE 134 131 131 ILE ILE A . n A 1 135 PHE 135 132 132 PHE PHE A . n A 1 136 GLY 136 133 133 GLY GLY A . n A 1 137 ALA 137 134 134 ALA ALA A . n A 1 138 ASP 138 135 135 ASP ASP A . n A 1 139 PRO 139 136 136 PRO PRO A . n A 1 140 ILE 140 137 137 ILE ILE A . n A 1 141 HIS 141 138 138 HIS HIS A . n A 1 142 SER 142 139 139 SER SER A . n A 1 143 LEU 143 140 140 LEU LEU A . n A 1 144 ARG 144 141 141 ARG ARG A . n A 1 145 VAL 145 142 142 VAL VAL A . n A 1 146 CYS 146 143 143 CYS CYS A . n A 1 147 VAL 147 144 144 VAL VAL A . n A 1 148 ASP 148 145 145 ASP ASP A . n A 1 149 THR 149 146 146 THR THR A . n A 1 150 VAL 150 147 147 VAL VAL A . n A 1 151 ARG 151 148 148 ARG ARG A . n A 1 152 THR 152 149 149 THR THR A . n A 1 153 ASN 153 150 150 ASN ASN A . n A 1 154 VAL 154 151 151 VAL VAL A . n A 1 155 TYR 155 152 152 TYR TYR A . n A 1 156 LEU 156 153 153 LEU LEU A . n A 1 157 ALA 157 154 154 ALA ALA A . n A 1 158 VAL 158 155 155 VAL VAL A . n A 1 159 PHE 159 156 156 PHE PHE A . n A 1 160 ASP 160 157 157 ASP ASP A . n A 1 161 LYS 161 158 158 LYS LYS A . n A 1 162 ASN 162 159 159 ASN ASN A . n A 1 163 LEU 163 160 160 LEU LEU A . n A 1 164 TYR 164 161 161 TYR TYR A . n A 1 165 ASP 165 162 162 ASP ASP A . n A 1 166 LYS 166 163 163 LYS LYS A . n A 1 167 LEU 167 164 164 LEU LEU A . n A 1 168 VAL 168 165 165 VAL VAL A . n A 1 169 SER 169 166 166 SER SER A . n A 1 170 SER 170 167 167 SER SER A . n A 1 171 PHE 171 168 168 PHE PHE A . n A 1 172 LEU 172 169 169 LEU LEU A . n A 1 173 GLU 173 170 170 GLU GLU A . n # 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 BVF 1 201 201 BVF LIG A . C 3 HOH 1 301 130 HOH HOH A . C 3 HOH 2 302 94 HOH HOH A . C 3 HOH 3 303 146 HOH HOH A . C 3 HOH 4 304 58 HOH HOH A . C 3 HOH 5 305 85 HOH HOH A . C 3 HOH 6 306 112 HOH HOH A . C 3 HOH 7 307 72 HOH HOH A . C 3 HOH 8 308 88 HOH HOH A . C 3 HOH 9 309 106 HOH HOH A . C 3 HOH 10 310 137 HOH HOH A . C 3 HOH 11 311 90 HOH HOH A . C 3 HOH 12 312 37 HOH HOH A . C 3 HOH 13 313 119 HOH HOH A . C 3 HOH 14 314 68 HOH HOH A . C 3 HOH 15 315 76 HOH HOH A . C 3 HOH 16 316 25 HOH HOH A . C 3 HOH 17 317 83 HOH HOH A . C 3 HOH 18 318 149 HOH HOH A . C 3 HOH 19 319 84 HOH HOH A . C 3 HOH 20 320 62 HOH HOH A . C 3 HOH 21 321 36 HOH HOH A . C 3 HOH 22 322 60 HOH HOH A . C 3 HOH 23 323 39 HOH HOH A . C 3 HOH 24 324 86 HOH HOH A . C 3 HOH 25 325 15 HOH HOH A . C 3 HOH 26 326 7 HOH HOH A . C 3 HOH 27 327 57 HOH HOH A . C 3 HOH 28 328 142 HOH HOH A . C 3 HOH 29 329 134 HOH HOH A . C 3 HOH 30 330 153 HOH HOH A . C 3 HOH 31 331 120 HOH HOH A . C 3 HOH 32 332 121 HOH HOH A . C 3 HOH 33 333 54 HOH HOH A . C 3 HOH 34 334 16 HOH HOH A . C 3 HOH 35 335 35 HOH HOH A . C 3 HOH 36 336 97 HOH HOH A . C 3 HOH 37 337 18 HOH HOH A . C 3 HOH 38 338 45 HOH HOH A . C 3 HOH 39 339 100 HOH HOH A . C 3 HOH 40 340 1 HOH HOH A . C 3 HOH 41 341 47 HOH HOH A . C 3 HOH 42 342 115 HOH HOH A . C 3 HOH 43 343 13 HOH HOH A . C 3 HOH 44 344 29 HOH HOH A . C 3 HOH 45 345 65 HOH HOH A . C 3 HOH 46 346 6 HOH HOH A . C 3 HOH 47 347 38 HOH HOH A . C 3 HOH 48 348 31 HOH HOH A . C 3 HOH 49 349 135 HOH HOH A . C 3 HOH 50 350 145 HOH HOH A . C 3 HOH 51 351 79 HOH HOH A . C 3 HOH 52 352 2 HOH HOH A . C 3 HOH 53 353 30 HOH HOH A . C 3 HOH 54 354 77 HOH HOH A . C 3 HOH 55 355 10 HOH HOH A . C 3 HOH 56 356 99 HOH HOH A . C 3 HOH 57 357 14 HOH HOH A . C 3 HOH 58 358 87 HOH HOH A . C 3 HOH 59 359 50 HOH HOH A . C 3 HOH 60 360 23 HOH HOH A . C 3 HOH 61 361 44 HOH HOH A . C 3 HOH 62 362 128 HOH HOH A . C 3 HOH 63 363 8 HOH HOH A . C 3 HOH 64 364 19 HOH HOH A . C 3 HOH 65 365 89 HOH HOH A . C 3 HOH 66 366 48 HOH HOH A . C 3 HOH 67 367 116 HOH HOH A . C 3 HOH 68 368 32 HOH HOH A . C 3 HOH 69 369 107 HOH HOH A . C 3 HOH 70 370 67 HOH HOH A . C 3 HOH 71 371 42 HOH HOH A . C 3 HOH 72 372 127 HOH HOH A . C 3 HOH 73 373 4 HOH HOH A . C 3 HOH 74 374 144 HOH HOH A . C 3 HOH 75 375 52 HOH HOH A . C 3 HOH 76 376 49 HOH HOH A . C 3 HOH 77 377 123 HOH HOH A . C 3 HOH 78 378 12 HOH HOH A . C 3 HOH 79 379 3 HOH HOH A . C 3 HOH 80 380 138 HOH HOH A . C 3 HOH 81 381 140 HOH HOH A . C 3 HOH 82 382 5 HOH HOH A . C 3 HOH 83 383 11 HOH HOH A . C 3 HOH 84 384 40 HOH HOH A . C 3 HOH 85 385 73 HOH HOH A . C 3 HOH 86 386 51 HOH HOH A . C 3 HOH 87 387 92 HOH HOH A . C 3 HOH 88 388 104 HOH HOH A . C 3 HOH 89 389 53 HOH HOH A . C 3 HOH 90 390 22 HOH HOH A . C 3 HOH 91 391 17 HOH HOH A . C 3 HOH 92 392 125 HOH HOH A . C 3 HOH 93 393 21 HOH HOH A . C 3 HOH 94 394 26 HOH HOH A . C 3 HOH 95 395 34 HOH HOH A . C 3 HOH 96 396 152 HOH HOH A . C 3 HOH 97 397 122 HOH HOH A . C 3 HOH 98 398 43 HOH HOH A . C 3 HOH 99 399 91 HOH HOH A . C 3 HOH 100 400 143 HOH HOH A . C 3 HOH 101 401 9 HOH HOH A . C 3 HOH 102 402 27 HOH HOH A . C 3 HOH 103 403 93 HOH HOH A . C 3 HOH 104 404 20 HOH HOH A . C 3 HOH 105 405 81 HOH HOH A . C 3 HOH 106 406 33 HOH HOH A . C 3 HOH 107 407 70 HOH HOH A . C 3 HOH 108 408 41 HOH HOH A . C 3 HOH 109 409 147 HOH HOH A . C 3 HOH 110 410 75 HOH HOH A . C 3 HOH 111 411 78 HOH HOH A . C 3 HOH 112 412 66 HOH HOH A . C 3 HOH 113 413 136 HOH HOH A . C 3 HOH 114 414 101 HOH HOH A . C 3 HOH 115 415 56 HOH HOH A . C 3 HOH 116 416 64 HOH HOH A . C 3 HOH 117 417 24 HOH HOH A . C 3 HOH 118 418 55 HOH HOH A . C 3 HOH 119 419 131 HOH HOH A . C 3 HOH 120 420 133 HOH HOH A . C 3 HOH 121 421 103 HOH HOH A . C 3 HOH 122 422 59 HOH HOH A . C 3 HOH 123 423 154 HOH HOH A . C 3 HOH 124 424 113 HOH HOH A . C 3 HOH 125 425 95 HOH HOH A . C 3 HOH 126 426 96 HOH HOH A . C 3 HOH 127 427 111 HOH HOH A . C 3 HOH 128 428 141 HOH HOH A . C 3 HOH 129 429 82 HOH HOH A . C 3 HOH 130 430 105 HOH HOH A . C 3 HOH 131 431 80 HOH HOH A . C 3 HOH 132 432 139 HOH HOH A . C 3 HOH 133 433 109 HOH HOH A . C 3 HOH 134 434 150 HOH HOH A . C 3 HOH 135 435 118 HOH HOH A . C 3 HOH 136 436 151 HOH HOH A . C 3 HOH 137 437 102 HOH HOH A . C 3 HOH 138 438 126 HOH HOH A . C 3 HOH 139 439 28 HOH HOH A . C 3 HOH 140 440 114 HOH HOH A . C 3 HOH 141 441 108 HOH HOH A . C 3 HOH 142 442 117 HOH HOH A . C 3 HOH 143 443 98 HOH HOH A . C 3 HOH 144 444 46 HOH HOH A . C 3 HOH 145 445 110 HOH HOH A . C 3 HOH 146 446 74 HOH HOH A . C 3 HOH 147 447 148 HOH HOH A . C 3 HOH 148 448 132 HOH HOH A . C 3 HOH 149 449 61 HOH HOH A . C 3 HOH 150 450 69 HOH HOH A . C 3 HOH 151 451 129 HOH HOH A . C 3 HOH 152 452 63 HOH HOH A . C 3 HOH 153 453 71 HOH HOH A . C 3 HOH 154 454 124 HOH HOH A . # _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_ _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 1 'Structure model' 1 0 2020-12-16 2 'Structure model' 1 1 2021-01-27 3 'Structure model' 1 2 2021-05-12 4 'Structure model' 1 3 2021-06-09 5 'Structure model' 1 4 2022-05-25 # _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 ? # 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 2 'Structure model' 'Structure summary' 2 3 'Structure model' 'Structure summary' 3 4 'Structure model' 'Structure summary' 4 5 'Structure model' 'Database references' # 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 2 'Structure model' entity 2 2 'Structure model' entity_name_com 3 3 'Structure model' pdbx_deposit_group 4 4 'Structure model' struct 5 5 'Structure model' citation 6 5 'Structure model' citation_author 7 5 'Structure model' database_2 # 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 2 'Structure model' '_entity.pdbx_ec' 2 2 'Structure model' '_entity_name_com.name' 3 3 'Structure model' '_pdbx_deposit_group.group_description' 4 3 'Structure model' '_pdbx_deposit_group.group_type' 5 4 'Structure model' '_struct.title' 6 5 'Structure model' '_citation.country' 7 5 'Structure model' '_citation.journal_abbrev' 8 5 'Structure model' '_citation.journal_id_CSD' 9 5 'Structure model' '_citation.journal_id_ISSN' 10 5 'Structure model' '_citation.journal_volume' 11 5 'Structure model' '_citation.pdbx_database_id_DOI' 12 5 'Structure model' '_citation.pdbx_database_id_PubMed' 13 5 'Structure model' '_citation.title' 14 5 'Structure model' '_citation.year' 15 5 'Structure model' '_database_2.pdbx_DOI' 16 5 'Structure model' '_database_2.pdbx_database_accession' # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 PHENIX 1.18.2_3874 ? package 'Paul D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 2 XSCALE . ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 3 PDB_EXTRACT 3.25 'Apr. 1, 2019' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 4 XDS 0.94 'Mar. 16, 2020' package 'Wolfgang Kabsch' Wolfgang.Kabsch@mpimf-heidelberg.mpg.de 'data reduction' http://xds.mpimf-heidelberg.mpg.de ? ? 5 PHASER 2.8.3 'May 17, 2020' package 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing https://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software ? ? # _pdbx_entry_details.entry_id 5RVL _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 HH12 A ARG 148 ? ? O A HOH 301 ? ? 1.34 2 1 NH1 A ARG 148 ? ? O A HOH 301 ? ? 1.93 3 1 O A HOH 398 ? ? O A HOH 439 ? ? 1.93 4 1 O A HOH 405 ? ? O A HOH 439 ? ? 2.00 5 1 O A HOH 384 ? ? O A HOH 402 ? ? 2.01 6 1 O A HOH 386 ? ? O A HOH 421 ? ? 2.03 7 1 O A HOH 429 ? ? O A HOH 450 ? ? 2.04 8 1 O A HOH 413 ? ? O A HOH 433 ? ? 2.15 9 1 O A HOH 306 ? ? O A HOH 434 ? ? 2.16 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 OD1 A ASN 101 ? ? 1_555 HH11 A ARG 148 ? ? 1_565 1.24 2 1 OD1 A ASN 101 ? ? 1_555 NH1 A ARG 148 ? ? 1_565 1.70 3 1 O A HOH 388 ? ? 1_555 O A HOH 430 ? ? 1_554 1.95 # 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 ASN A 59 ? ? 85.83 3.80 2 1 HIS A 86 ? ? 55.65 -130.60 # 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 SER -2 ? A SER 1 2 1 Y 1 A ASN -1 ? A ASN 2 3 1 Y 1 A ALA 0 ? A ALA 3 4 1 Y 1 A GLY 1 ? A GLY 4 5 1 Y 1 A GLU 2 ? A GLU 5 # _pdbx_audit_support.funding_organization 'National Science Foundation' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number 2031205 _pdbx_audit_support.ordinal 1 # _pdbx_deposit_group.group_title 'PanDDA analysis group deposition of SARS-CoV-2 NSP3 macrodomain fragment screen' _pdbx_deposit_group.group_description ;SARS-CoV-2 NSP3 macrodomain from SARS-CoV-2 screened against the Enamine Essential fragment library (Enamine) and the UCSF_91 fragment library (UCSF) by X-ray Crystallography at UCSF using ALS 8.3.1 and SSRL 12-2 ; _pdbx_deposit_group.group_id G_1002172 _pdbx_deposit_group.group_type undefined # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id BVF _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id BVF _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_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 4-METHYLPYRIDIN-2-AMINE BVF 3 water HOH #