data_5S50 # _model_server_result.job_id CnP7CuQDwFLxHIAhqXAMVQ _model_server_result.datetime_utc '2024-11-07 16:44:34' _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 5s50 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":505}' # _entry.id 5S50 # _exptl.entry_id 5S50 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 213.235 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(furan-2-yl)methyl]-1H-benzimidazol-2-amine _entity.pdbx_number_of_molecules 2 _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 5S50 _cell.length_a 104.03 _cell.length_b 158.02 _cell.length_c 180.88 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5S50 _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 ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 10 O N N ? 10 U 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 metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc8 A OE1 GLU 71 A GLU 71 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc9 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc10 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? metalc ? metalc11 H MG MG . A MG 502 1_555 X O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.807 ? metalc ? metalc12 H MG MG . A MG 502 1_555 X O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.837 ? metalc ? metalc13 I CA CA . A CA 503 1_555 X O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc14 J CA CA . A CA 504 1_555 BA O HOH . E HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? metalc ? metalc15 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc16 B OE1 GLU 111 B GLU 113 1_555 M CA CA . B CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? metalc ? metalc17 L MG MG . B MG 502 1_555 Y O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc18 L MG MG . B MG 502 1_555 Y O HOH . B HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc19 L MG MG . B MG 502 1_555 Y O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc20 M CA CA . B CA 503 4_455 C OE1 GLU 284 C GLU 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.189 ? metalc ? metalc21 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc22 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc23 C O THR 41 C THR 41 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc24 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc25 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc26 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? metalc ? metalc27 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc28 P O1G GTP . C GTP 501 1_555 R MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc29 P O1B GTP . C GTP 501 1_555 R MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc30 Q CA CA . C CA 502 1_555 Z O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc31 Z O HOH . C HOH 602 1_555 R MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc32 Z O HOH . C HOH 605 1_555 R MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc33 D OE1 GLN 11 D GLN 11 1_555 T MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc34 T MG MG . D MG 503 1_555 AA O HOH . D HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc35 F OE2 GLU 331 F GLU 331 1_555 W MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? metalc ? metalc36 V O1B ACP . F ACP 401 1_555 W MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? # _chem_comp.formula 'C12 H11 N3 O' _chem_comp.formula_weight 213.235 _chem_comp.id WZD _chem_comp.mon_nstd_flag . _chem_comp.name N-[(furan-2-yl)methyl]-1H-benzimidazol-2-amine _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 CAO CAN WZD doub 547 n y CAO CAP WZD sing 548 n y CAN OAM WZD sing 549 n y CAP CAL WZD doub 550 n y OAM CAL WZD sing 551 n y CAL CAK WZD sing 552 n n CAK NAJ WZD sing 553 n n NAJ CAH WZD sing 554 n n CAH NAG WZD doub 555 n y CAH NAI WZD sing 556 n y NAG CAE WZD sing 557 n y NAI CAF WZD sing 558 n y CAE CAF WZD doub 559 n y CAE CAD WZD sing 560 n y CAF CAA WZD sing 561 n y CAD CAC WZD doub 562 n y CAA CAB WZD doub 563 n y CAC CAB WZD sing 564 n y CAA HAA WZD sing 565 n n CAB HAB WZD sing 566 n n CAC HAC WZD sing 567 n n CAD HAD WZD sing 568 n n CAK HAL WZD sing 569 n n CAK HAK WZD sing 570 n n CAN HAN WZD sing 571 n n CAO HAO WZD sing 572 n n CAP HAP WZD sing 573 n n NAI HAI WZD sing 574 n n NAJ HAJ WZD sing 575 n n # _atom_sites.entry_id 5S50 _atom_sites.fract_transf_matrix[1][1] 0.009613 _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] 0.006328 _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] 0.005529 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 7 CA A 1 504 504 CA CA . K 8 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 7 CA B 1 503 503 CA CA . N 9 MES B 1 504 504 MES MES . O 10 WZD B 1 505 601 WZD DRG . P 5 GTP C 1 501 501 GTP GTP . Q 7 CA C 1 502 503 CA CA . R 6 MG D 1 501 502 MG MG . S 8 GDP D 1 502 501 GDP GDP . T 6 MG D 1 503 502 MG MG . U 10 WZD D 1 504 601 WZD DRG . V 11 ACP F 1 401 401 ACP ACP . W 6 MG F 1 402 402 MG MG . X 12 HOH A 1 601 180 HOH HOH . X 12 HOH A 2 602 22 HOH HOH . X 12 HOH A 3 603 78 HOH HOH . X 12 HOH A 4 604 135 HOH HOH . Y 12 HOH B 1 601 440 HOH HOH . Y 12 HOH B 2 602 405 HOH HOH . Y 12 HOH B 3 603 345 HOH HOH . Y 12 HOH B 4 604 1335 HOH HOH . Z 12 HOH C 1 601 641 HOH HOH . Z 12 HOH C 2 602 732 HOH HOH . Z 12 HOH C 3 603 800 HOH HOH . Z 12 HOH C 4 604 664 HOH HOH . Z 12 HOH C 5 605 888 HOH HOH . Z 12 HOH C 6 606 995 HOH HOH . Z 12 HOH C 7 607 931 HOH HOH . Z 12 HOH C 8 608 1000 HOH HOH . Z 12 HOH C 9 609 938 HOH HOH . Z 12 HOH C 10 610 436 HOH HOH . Z 12 HOH C 11 611 874 HOH HOH . Z 12 HOH C 12 612 963 HOH HOH . AA 12 HOH D 1 601 1200 HOH HOH . AA 12 HOH D 2 602 1222 HOH HOH . BA 12 HOH E 1 201 1334 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 CAA WZD . . . O 10 17.321 63.857 39.668 1 113.21 ? CAA WZD 505 B 1 HETATM 2 C CAB WZD . . . O 10 16.301 64.278 40.507 1 120.33 ? CAB WZD 505 B 1 HETATM 3 C CAC WZD . . . O 10 15.201 64.917 39.958 1 118.68 ? CAC WZD 505 B 1 HETATM 4 C CAD WZD . . . O 10 15.162 65.111 38.586 1 117.17 ? CAD WZD 505 B 1 HETATM 5 C CAE WZD . . . O 10 16.168 64.687 37.825 1 117.73 ? CAE WZD 505 B 1 HETATM 6 C CAF WZD . . . O 10 17.232 64.069 38.358 1 113.93 ? CAF WZD 505 B 1 HETATM 7 C CAH WZD . . . O 10 17.509 64.185 36.251 1 111.94 ? CAH WZD 505 B 1 HETATM 8 C CAK WZD . . . O 10 17.335 64.562 33.849 1 115.54 ? CAK WZD 505 B 1 HETATM 9 C CAL WZD . . . O 10 18.236 64.377 32.638 1 107.42 ? CAL WZD 505 B 1 HETATM 10 C CAN WZD . . . O 10 19.776 63.658 31.351 1 109.65 ? CAN WZD 505 B 1 HETATM 11 C CAO WZD . . . O 10 19.111 64.62 30.713 1 108.37 ? CAO WZD 505 B 1 HETATM 12 C CAP WZD . . . O 10 18.15 65.072 31.516 1 104.94 ? CAP WZD 505 B 1 HETATM 13 N NAG WZD . . . O 10 16.347 64.764 36.51 1 111 ? NAG WZD 505 B 1 HETATM 14 N NAI WZD . . . O 10 18.073 63.767 37.372 1 113.46 ? NAI WZD 505 B 1 HETATM 15 N NAJ WZD . . . O 10 18.038 64.068 35.041 1 116.11 ? NAJ WZD 505 B 1 HETATM 16 O OAM WZD . . . O 10 19.22 63.507 32.573 1 111.4 ? OAM WZD 505 B 1 HETATM 17 H HAA WZD . . . O 10 18.195 63.353 40.082 1 136.17 ? HAA WZD 505 B 1 HETATM 18 H HAB WZD . . . O 10 16.363 64.11 41.583 1 144.72 ? HAB WZD 505 B 1 HETATM 19 H HAC WZD . . . O 10 14.382 65.259 40.591 1 142.74 ? HAC WZD 505 B 1 HETATM 20 H HAD WZD . . . O 10 14.307 65.611 38.13 1 140.92 ? HAD WZD 505 B 1 HETATM 21 H HAL WZD . . . O 10 16.412 63.999 33.709 1 138.97 ? HAL WZD 505 B 1 HETATM 22 H HAK WZD . . . O 10 17.101 65.619 33.974 1 138.97 ? HAK WZD 505 B 1 HETATM 23 H HAN WZD . . . O 10 20.62 63.092 30.957 1 131.9 ? HAN WZD 505 B 1 HETATM 24 H HAO WZD . . . O 10 19.318 64.977 29.704 1 130.37 ? HAO WZD 505 B 1 HETATM 25 H HAP WZD . . . O 10 17.433 65.861 31.292 1 126.25 ? HAP WZD 505 B 1 HETATM 26 H HAI WZD . . . O 10 18.959 63.313 37.462 1 136.48 ? HAI WZD 505 B 1 HETATM 27 H HAJ WZD . . . O 10 18.927 63.645 34.869 1 139.66 ? HAJ WZD 505 B 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #