data_6AVL # _model_server_result.job_id riMmD8q4vtQo86JgsNgpwg _model_server_result.datetime_utc '2024-11-23 05:34:59' _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 6avl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 6AVL # _exptl.entry_id 6AVL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 120.152 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description BENZAMIDINE _entity.pdbx_number_of_molecules 1 _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 6AVL _cell.length_a 54.87 _cell.length_b 58.756 _cell.length_c 67.484 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6AVL _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 x,y,z _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 7 A CYS 22 1_555 A SG CYS 137 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 41 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 A SG CYS 109 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf4 A SG CYS 116 A CYS 136 1_555 A SG CYS 183 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf5 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf6 A SG CYS 173 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc1 A OE1 GLU 52 A GLU 70 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc2 A O ASN 54 A ASN 72 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc3 A O VAL 57 A VAL 75 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc4 A OE2 GLU 62 A GLU 80 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc5 B CA CA . A CA 301 1_555 G O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc6 B CA CA . A CA 301 1_555 G O HOH . A HOH 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? # _chem_comp.formula 'C7 H8 N2' _chem_comp.formula_weight 120.152 _chem_comp.id BEN _chem_comp.mon_nstd_flag . _chem_comp.name BENZAMIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C1 C2 BEN doub 70 n y C1 C6 BEN sing 71 n y C1 C BEN sing 72 n n C2 C3 BEN sing 73 n y C2 H2 BEN sing 74 n n C3 C4 BEN doub 75 n y C3 H3 BEN sing 76 n n C4 C5 BEN sing 77 n y C4 H4 BEN sing 78 n n C5 C6 BEN doub 79 n y C5 H5 BEN sing 80 n n C6 H6 BEN sing 81 n n C N1 BEN doub 82 e n C N2 BEN sing 83 n n N1 HN1 BEN sing 84 n n N2 HN21 BEN sing 85 n n N2 HN22 BEN sing 86 n n # _atom_sites.entry_id 6AVL _atom_sites.fract_transf_matrix[1][1] 0.018225 _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] 0.01702 _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] 0.014818 _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 B 2 CA A 1 301 301 CA CA . C 3 BEN A 1 302 302 BEN BEN . D 4 SO4 A 1 303 303 SO4 SO4 . E 5 XYP A 1 304 311 XYP XYP . F 6 XYS A 1 305 312 XYS XYS . G 7 HOH A 1 401 1175 HOH HOH . G 7 HOH A 2 402 1002 HOH HOH . G 7 HOH A 3 403 1029 HOH HOH . G 7 HOH A 4 404 1105 HOH HOH . G 7 HOH A 5 405 1301 HOH HOH . G 7 HOH A 6 406 1402 HOH HOH . G 7 HOH A 7 407 1016 HOH HOH . G 7 HOH A 8 408 1032 HOH HOH . G 7 HOH A 9 409 1073 HOH HOH . G 7 HOH A 10 410 1125 HOH HOH . G 7 HOH A 11 411 1405 HOH HOH . G 7 HOH A 12 412 1041 HOH HOH . G 7 HOH A 13 413 1385 HOH HOH . G 7 HOH A 14 414 1235 HOH HOH . G 7 HOH A 15 415 1071 HOH HOH . G 7 HOH A 16 416 1231 HOH HOH . G 7 HOH A 17 417 1180 HOH HOH . G 7 HOH A 18 418 1018 HOH HOH . G 7 HOH A 19 419 1070 HOH HOH . G 7 HOH A 20 420 1117 HOH HOH . G 7 HOH A 21 421 1166 HOH HOH . G 7 HOH A 22 422 1065 HOH HOH . G 7 HOH A 23 423 1076 HOH HOH . G 7 HOH A 24 424 1234 HOH HOH . G 7 HOH A 25 425 1035 HOH HOH . G 7 HOH A 26 426 1034 HOH HOH . G 7 HOH A 27 427 1030 HOH HOH . G 7 HOH A 28 428 1167 HOH HOH . G 7 HOH A 29 429 1112 HOH HOH . G 7 HOH A 30 430 1013 HOH HOH . G 7 HOH A 31 431 1103 HOH HOH . G 7 HOH A 32 432 1019 HOH HOH . G 7 HOH A 33 433 1052 HOH HOH . G 7 HOH A 34 434 1426 HOH HOH . G 7 HOH A 35 435 1072 HOH HOH . G 7 HOH A 36 436 1010 HOH HOH . G 7 HOH A 37 437 1049 HOH HOH . G 7 HOH A 38 438 1003 HOH HOH . G 7 HOH A 39 439 1047 HOH HOH . G 7 HOH A 40 440 1001 HOH HOH . G 7 HOH A 41 441 1171 HOH HOH . G 7 HOH A 42 442 1366 HOH HOH . G 7 HOH A 43 443 1408 HOH HOH . G 7 HOH A 44 444 1006 HOH HOH . G 7 HOH A 45 445 1060 HOH HOH . G 7 HOH A 46 446 1027 HOH HOH . G 7 HOH A 47 447 1206 HOH HOH . G 7 HOH A 48 448 1425 HOH HOH . G 7 HOH A 49 449 1432 HOH HOH . G 7 HOH A 50 450 1025 HOH HOH . G 7 HOH A 51 451 1069 HOH HOH . G 7 HOH A 52 452 1014 HOH HOH . G 7 HOH A 53 453 1202 HOH HOH . G 7 HOH A 54 454 1189 HOH HOH . G 7 HOH A 55 455 1033 HOH HOH . G 7 HOH A 56 456 1017 HOH HOH . G 7 HOH A 57 457 1044 HOH HOH . G 7 HOH A 58 458 1042 HOH HOH . G 7 HOH A 59 459 1113 HOH HOH . G 7 HOH A 60 460 1063 HOH HOH . G 7 HOH A 61 461 1066 HOH HOH . G 7 HOH A 62 462 1133 HOH HOH . G 7 HOH A 63 463 1095 HOH HOH . G 7 HOH A 64 464 1415 HOH HOH . G 7 HOH A 65 465 1110 HOH HOH . G 7 HOH A 66 466 1024 HOH HOH . G 7 HOH A 67 467 1444 HOH HOH . G 7 HOH A 68 468 1015 HOH HOH . G 7 HOH A 69 469 1021 HOH HOH . G 7 HOH A 70 470 1008 HOH HOH . G 7 HOH A 71 471 1050 HOH HOH . G 7 HOH A 72 472 1369 HOH HOH . G 7 HOH A 73 473 1106 HOH HOH . G 7 HOH A 74 474 1040 HOH HOH . G 7 HOH A 75 475 1011 HOH HOH . G 7 HOH A 76 476 1005 HOH HOH . G 7 HOH A 77 477 1056 HOH HOH . G 7 HOH A 78 478 1099 HOH HOH . G 7 HOH A 79 479 1059 HOH HOH . G 7 HOH A 80 480 1061 HOH HOH . G 7 HOH A 81 481 1020 HOH HOH . G 7 HOH A 82 482 1023 HOH HOH . G 7 HOH A 83 483 1093 HOH HOH . G 7 HOH A 84 484 1022 HOH HOH . G 7 HOH A 85 485 1445 HOH HOH . G 7 HOH A 86 486 1220 HOH HOH . G 7 HOH A 87 487 1078 HOH HOH . G 7 HOH A 88 488 1232 HOH HOH . G 7 HOH A 89 489 1026 HOH HOH . G 7 HOH A 90 490 1122 HOH HOH . G 7 HOH A 91 491 1048 HOH HOH . G 7 HOH A 92 492 1282 HOH HOH . G 7 HOH A 93 493 1428 HOH HOH . G 7 HOH A 94 494 1054 HOH HOH . G 7 HOH A 95 495 1238 HOH HOH . G 7 HOH A 96 496 1152 HOH HOH . G 7 HOH A 97 497 1412 HOH HOH . G 7 HOH A 98 498 1083 HOH HOH . G 7 HOH A 99 499 1057 HOH HOH . G 7 HOH A 100 500 1286 HOH HOH . G 7 HOH A 101 501 1028 HOH HOH . G 7 HOH A 102 502 1009 HOH HOH . G 7 HOH A 103 503 1406 HOH HOH . G 7 HOH A 104 504 1045 HOH HOH . G 7 HOH A 105 505 1153 HOH HOH . G 7 HOH A 106 506 1089 HOH HOH . G 7 HOH A 107 507 1043 HOH HOH . G 7 HOH A 108 508 1007 HOH HOH . G 7 HOH A 109 509 1268 HOH HOH . G 7 HOH A 110 510 1139 HOH HOH . G 7 HOH A 111 511 1031 HOH HOH . G 7 HOH A 112 512 1039 HOH HOH . G 7 HOH A 113 513 1416 HOH HOH . G 7 HOH A 114 514 1255 HOH HOH . G 7 HOH A 115 515 1053 HOH HOH . G 7 HOH A 116 516 1233 HOH HOH . G 7 HOH A 117 517 1004 HOH HOH . G 7 HOH A 118 518 1012 HOH HOH . G 7 HOH A 119 519 1182 HOH HOH . G 7 HOH A 120 520 1037 HOH HOH . G 7 HOH A 121 521 1146 HOH HOH . G 7 HOH A 122 522 1401 HOH HOH . G 7 HOH A 123 523 1433 HOH HOH . G 7 HOH A 124 524 1176 HOH HOH . G 7 HOH A 125 525 1384 HOH HOH . G 7 HOH A 126 526 1446 HOH HOH . G 7 HOH A 127 527 1150 HOH HOH . G 7 HOH A 128 528 1062 HOH HOH . G 7 HOH A 129 529 1411 HOH HOH . G 7 HOH A 130 530 1410 HOH HOH . G 7 HOH A 131 531 1421 HOH HOH . G 7 HOH A 132 532 1038 HOH HOH . G 7 HOH A 133 533 1403 HOH HOH . G 7 HOH A 134 534 1036 HOH HOH . G 7 HOH A 135 535 1431 HOH HOH . G 7 HOH A 136 536 1085 HOH HOH . G 7 HOH A 137 537 1104 HOH HOH . G 7 HOH A 138 538 1131 HOH HOH . G 7 HOH A 139 539 1135 HOH HOH . G 7 HOH A 140 540 1100 HOH HOH . G 7 HOH A 141 541 1429 HOH HOH . G 7 HOH A 142 542 1367 HOH HOH . G 7 HOH A 143 543 1046 HOH HOH . G 7 HOH A 144 544 1149 HOH HOH . G 7 HOH A 145 545 1427 HOH HOH . G 7 HOH A 146 546 1260 HOH HOH . G 7 HOH A 147 547 1092 HOH HOH . G 7 HOH A 148 548 1365 HOH HOH . G 7 HOH A 149 549 1407 HOH HOH . G 7 HOH A 150 550 1114 HOH HOH . G 7 HOH A 151 551 1086 HOH HOH . G 7 HOH A 152 552 1340 HOH HOH . G 7 HOH A 153 553 1188 HOH HOH . G 7 HOH A 154 554 1090 HOH HOH . G 7 HOH A 155 555 1158 HOH HOH . G 7 HOH A 156 556 1284 HOH HOH . G 7 HOH A 157 557 1183 HOH HOH . G 7 HOH A 158 558 1430 HOH HOH . G 7 HOH A 159 559 1107 HOH HOH . G 7 HOH A 160 560 1409 HOH HOH . G 7 HOH A 161 561 1423 HOH HOH . G 7 HOH A 162 562 1221 HOH HOH . G 7 HOH A 163 563 1123 HOH HOH . G 7 HOH A 164 564 1145 HOH HOH . G 7 HOH A 165 565 1172 HOH HOH . G 7 HOH A 166 566 1087 HOH HOH . G 7 HOH A 167 567 1067 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 C C1 BEN . . . C 3 -1.793 -14.869 -17.117 1 15.67 ? C1 BEN 302 A 1 HETATM 2 C C2 BEN . . . C 3 -1.248 -15.531 -16.028 1 15.19 ? C2 BEN 302 A 1 HETATM 3 C C3 BEN . . . C 3 -0.946 -14.839 -14.855 1 11.84 ? C3 BEN 302 A 1 HETATM 4 C C4 BEN . . . C 3 -1.209 -13.478 -14.768 1 14.85 ? C4 BEN 302 A 1 HETATM 5 C C5 BEN . . . C 3 -1.735 -12.803 -15.857 1 15.76 ? C5 BEN 302 A 1 HETATM 6 C C6 BEN . . . C 3 -2.033 -13.501 -17.028 1 19.94 ? C6 BEN 302 A 1 HETATM 7 C C BEN . . . C 3 -2.1 -15.582 -18.299 1 10.29 ? C BEN 302 A 1 HETATM 8 N N1 BEN . . . C 3 -1.697 -16.827 -18.496 1 12.74 ? N1 BEN 302 A 1 HETATM 9 N N2 BEN . . . C 3 -2.823 -15.031 -19.247 1 10.79 ? N2 BEN 302 A 1 HETATM 10 H H2 BEN . . . C 3 -1.054 -16.601 -16.088 1 18.23 ? H2 BEN 302 A 1 HETATM 11 H H3 BEN . . . C 3 -0.573 -15.379 -13.985 1 14.21 ? H3 BEN 302 A 1 HETATM 12 H H4 BEN . . . C 3 -1.001 -12.941 -13.843 1 17.82 ? H4 BEN 302 A 1 HETATM 13 H H5 BEN . . . C 3 -1.837 -11.718 -15.828 1 18.91 ? H5 BEN 302 A 1 HETATM 14 H H6 BEN . . . C 3 -2.456 -12.97 -17.881 1 23.93 ? H6 BEN 302 A 1 HETATM 15 H HN21 BEN . . . C 3 -2.545 -15.13 -20.219 1 12.95 ? HN21 BEN 302 A 1 HETATM 16 H HN22 BEN . . . C 3 -3.661 -14.511 -19.009 1 12.95 ? HN22 BEN 302 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 467 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 16 #