data_8JV8 # _model_server_result.job_id iwSg-X8HNa53gt_9jWuwvA _model_server_result.datetime_utc '2024-11-22 14:27:29' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 8jv8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":403}' # _entry.id 8JV8 # _exptl.entry_id 8JV8 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 606.434 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]-7-nitronaphthalene-1,5-disulfonic acid' _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 8JV8 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JV8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 I N N ? 3 L N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 99 A CYS 119 1_555 A SG CYS 148 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 109 A CYS 129 1_555 A SG CYS 132 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 115 A CYS 135 1_555 A SG CYS 142 A CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 196 A CYS 216 1_555 A SG CYS 206 A CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 240 A CYS 260 1_555 A SG CYS 249 A CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 B SG CYS 99 B CYS 119 1_555 B SG CYS 148 B CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf7 B SG CYS 109 B CYS 129 1_555 B SG CYS 132 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf8 B SG CYS 115 B CYS 135 1_555 B SG CYS 142 B CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 B SG CYS 196 B CYS 216 1_555 B SG CYS 206 B CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf10 B SG CYS 240 B CYS 260 1_555 B SG CYS 249 B CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf11 C SG CYS 99 C CYS 119 1_555 C SG CYS 148 C CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 C SG CYS 109 C CYS 129 1_555 C SG CYS 132 C CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf13 C SG CYS 115 C CYS 135 1_555 C SG CYS 142 C CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf14 C SG CYS 196 C CYS 216 1_555 C SG CYS 206 C CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf15 C SG CYS 240 C CYS 260 1_555 C SG CYS 249 C CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? covale ? covale1 A ND2 ASN 167 A ASN 187 1_555 D C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale2 A ND2 ASN 193 A ASN 213 1_555 E C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale3 B ND2 ASN 167 B ASN 187 1_555 G C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale4 B ND2 ASN 193 B ASN 213 1_555 H C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale5 C ND2 ASN 167 C ASN 187 1_555 J C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 C ND2 ASN 193 C ASN 213 1_555 K C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? # _chem_comp.formula 'C18 H15 N4 O14 P S2' _chem_comp.formula_weight 606.434 _chem_comp.id 20V _chem_comp.mon_nstd_flag . _chem_comp.name '3-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]-7-nitronaphthalene-1,5-disulfonic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "PPNDS;Pyridoxal-5'-phosphate-6-(2'-naphthylazo-6'-nitro-4',8'-disulfonic acid)" # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag OAF SBM 20V doub 1 n n OAG SBM 20V doub 2 n n SBM OAN 20V sing 3 n n SBM CBG 20V sing 4 n n CBG CAQ 20V doub 5 n y CBG CBH 20V sing 6 n y CAQ CBB 20V sing 7 n y OAJ NBJ 20V sing 8 n n CAR CBH 20V doub 9 n y CAR CAZ 20V sing 10 n y CBH CBI 20V sing 11 n y CAA CAY 20V sing 12 n n CBB NBJ 20V sing 13 n n CBB CAS 20V doub 14 n y NBJ OAI 20V doub 15 n n NAW CAY 20V doub 16 n y NAW CBD 20V sing 17 n y CAY CBA 20V sing 18 n y NAU CAZ 20V sing 19 n n NAU NAV 20V doub 20 n n CAZ CAP 20V doub 21 n y CBI CAS 20V sing 22 n y CBI CBF 20V doub 23 n y NAV CBD 20V sing 24 n n CBD CBE 20V doub 25 n y CBA OAH 20V sing 26 n n CBA CBC 20V doub 27 n y CBE CBC 20V sing 28 n y CBE CAT 20V sing 29 n n CBC CAO 20V sing 30 n n CAP CBF 20V sing 31 n y OAB CAO 20V doub 32 n n CBF SBL 20V sing 33 n n CAT OAX 20V sing 34 n n OAM SBL 20V doub 35 n n SBL OAD 20V doub 36 n n SBL OAE 20V sing 37 n n OAX PBK 20V sing 38 n n OAL PBK 20V doub 39 n n PBK OAC 20V sing 40 n n PBK OAK 20V sing 41 n n OAK H1 20V sing 42 n n OAC H2 20V sing 43 n n CAT H3 20V sing 44 n n CAT H4 20V sing 45 n n CAO H5 20V sing 46 n n OAH H6 20V sing 47 n n CAA H7 20V sing 48 n n CAA H8 20V sing 49 n n CAA H9 20V sing 50 n n CAR H10 20V sing 51 n n CAQ H11 20V sing 52 n n CAS H12 20V sing 53 n n CAP H13 20V sing 54 n n OAN H14 20V sing 55 n n OAE H15 20V sing 56 n n # _atom_sites.entry_id 8JV8 _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code D 2 NAG A 1 401 401 NAG NAG . E 2 NAG A 1 402 402 NAG NAG . F 3 20V A 1 403 405 20V PPN . G 2 NAG B 1 401 401 NAG NAG . H 2 NAG B 1 402 402 NAG NAG . I 3 20V B 1 403 405 20V PPN . J 2 NAG C 1 401 401 NAG NAG . K 2 NAG C 1 402 402 NAG NAG . L 3 20V C 1 403 405 20V PPN . M 4 HOH A 1 501 404 HOH HOH . N 4 HOH B 1 501 404 HOH HOH . O 4 HOH C 1 501 404 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O OAK 20V . . . I 3 98.976 125.05 86.06 1 190.11 ? OAK 20V 403 B 1 HETATM 2 P PBK 20V . . . I 3 97.52 125.41 85.896 1 197.22 ? PBK 20V 403 B 1 HETATM 3 O OAL 20V . . . I 3 97.4 126.883 85.584 1 193.47 ? OAL 20V 403 B 1 HETATM 4 O OAC 20V . . . I 3 96.935 124.607 84.76 1 191.87 ? OAC 20V 403 B 1 HETATM 5 O OAX 20V . . . I 3 96.722 125.07 87.299 1 193.9 ? OAX 20V 403 B 1 HETATM 6 C CAT 20V . . . I 3 95.479 124.425 87.252 1 190.02 ? CAT 20V 403 B 1 HETATM 7 C CBE 20V . . . I 3 94.492 125.244 86.424 1 188.82 ? CBE 20V 403 B 1 HETATM 8 C CBC 20V . . . I 3 93.747 124.652 85.467 1 187.94 ? CBC 20V 403 B 1 HETATM 9 C CAO 20V . . . I 3 93.883 123.17 85.21 1 188.88 ? CAO 20V 403 B 1 HETATM 10 O OAB 20V . . . I 3 93.082 122.66 84.506 1 190.61 ? OAB 20V 403 B 1 HETATM 11 C CBA 20V . . . I 3 92.87 125.366 84.727 1 189.79 ? CBA 20V 403 B 1 HETATM 12 O OAH 20V . . . I 3 92.107 124.729 83.738 1 191.04 ? OAH 20V 403 B 1 HETATM 13 C CAY 20V . . . I 3 92.735 126.723 84.955 1 190.53 ? CAY 20V 403 B 1 HETATM 14 C CAA 20V . . . I 3 91.75 127.554 84.145 1 189.39 ? CAA 20V 403 B 1 HETATM 15 N NAW 20V . . . I 3 93.474 127.319 85.907 1 191 ? NAW 20V 403 B 1 HETATM 16 C CBD 20V . . . I 3 94.346 126.597 86.64 1 190.95 ? CBD 20V 403 B 1 HETATM 17 N NAV 20V . . . I 3 95.119 127.269 87.653 1 191.95 ? NAV 20V 403 B 1 HETATM 18 N NAU 20V . . . I 3 94.955 128.459 87.757 1 190.13 ? NAU 20V 403 B 1 HETATM 19 C CAZ 20V . . . I 3 95.657 129.201 88.777 1 188.93 ? CAZ 20V 403 B 1 HETATM 20 C CAR 20V . . . I 3 95.493 130.536 88.895 1 188.87 ? CAR 20V 403 B 1 HETATM 21 C CBH 20V . . . I 3 96.159 131.204 89.927 1 189.27 ? CBH 20V 403 B 1 HETATM 22 C CBG 20V . . . I 3 95.99 132.504 90.006 1 191.34 ? CBG 20V 403 B 1 HETATM 23 S SBM 20V . . . I 3 94.917 133.243 88.748 1 197.96 ? SBM 20V 403 B 1 HETATM 24 O OAN 20V . . . I 3 93.518 132.682 88.844 1 193.79 ? OAN 20V 403 B 1 HETATM 25 O OAG 20V . . . I 3 94.908 134.745 88.872 1 194.04 ? OAG 20V 403 B 1 HETATM 26 O OAF 20V . . . I 3 95.511 133.072 87.367 1 190.3 ? OAF 20V 403 B 1 HETATM 27 C CAQ 20V . . . I 3 96.579 133.375 90.978 1 192.25 ? CAQ 20V 403 B 1 HETATM 28 C CBB 20V . . . I 3 97.452 132.666 91.97 1 190.76 ? CBB 20V 403 B 1 HETATM 29 N NBJ 20V . . . I 3 98.155 133.319 93.052 0 190.17 ? NBJ 20V 403 B 1 HETATM 30 O OAJ 20V . . . I 3 97.86 132.984 94.383 0 190 ? OAJ 20V 403 B 1 HETATM 31 O OAI 20V . . . I 3 98.966 134.131 92.813 0 190.2 ? OAI 20V 403 B 1 HETATM 32 C CAS 20V . . . I 3 97.516 131.262 91.735 1 190.78 ? CAS 20V 403 B 1 HETATM 33 C CBI 20V . . . I 3 96.911 130.586 90.78 1 190.02 ? CBI 20V 403 B 1 HETATM 34 C CBF 20V . . . I 3 97.083 129.21 90.688 1 190.29 ? CBF 20V 403 B 1 HETATM 35 S SBL 20V . . . I 3 98.137 128.307 91.881 1 193.88 ? SBL 20V 403 B 1 HETATM 36 O OAM 20V . . . I 3 98.997 129.156 92.769 1 193.89 ? OAM 20V 403 B 1 HETATM 37 O OAE 20V . . . I 3 97.281 127.492 92.827 1 189.38 ? OAE 20V 403 B 1 HETATM 38 O OAD 20V . . . I 3 99.043 127.335 91.154 1 187.79 ? OAD 20V 403 B 1 HETATM 39 C CAP 20V . . . I 3 96.435 128.57 89.668 1 189.27 ? CAP 20V 403 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #