data_3VYW # _model_server_result.job_id vijAFaLG0YM_d4JEPcgc-g _model_server_result.datetime_utc '2024-11-04 22:53:02' _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 3vyw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":402}' # _entry.id 3VYW # _exptl.entry_id 3VYW _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.44 _cell.angle_gamma 90 _cell.entry_id 3VYW _cell.length_a 55.487 _cell.length_b 107.581 _cell.length_c 117.711 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VYW _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,K 1 1 B,F,G,L 2 1 C,H,I,M 3 1 D,J,N 4 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 ? 3 G N N ? 3 I 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 covale ? covale1 A C PRO 265 A PRO 265 1_555 A N MSE 266 A MSE 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale2 A C MSE 266 A MSE 266 1_555 A N GLU 267 A GLU 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.271 ? covale ? covale3 A C PRO 282 A PRO 282 1_555 A N MSE 283 A MSE 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.246 ? covale ? covale4 A C MSE 283 A MSE 283 1_555 A N ARG 284 A ARG 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 B C PRO 265 B PRO 265 1_555 B N MSE 266 B MSE 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale6 B C MSE 266 B MSE 266 1_555 B N GLU 267 B GLU 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.255 ? covale ? covale7 B C PRO 282 B PRO 282 1_555 B N MSE 283 B MSE 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.276 ? covale ? covale8 B C MSE 283 B MSE 283 1_555 B N ARG 284 B ARG 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale9 C C PRO 265 C PRO 265 1_555 C N MSE 266 C MSE 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.302 ? covale ? covale10 C C MSE 266 C MSE 266 1_555 C N GLU 267 C GLU 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.251 ? covale ? covale11 C C PRO 282 C PRO 282 1_555 C N MSE 283 C MSE 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.26 ? covale ? covale12 C C MSE 283 C MSE 283 1_555 C N ARG 284 C ARG 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.263 ? covale ? covale13 D C PRO 265 D PRO 265 1_555 D N MSE 266 D MSE 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.278 ? covale ? covale14 D C MSE 266 D MSE 266 1_555 D N GLU 267 D GLU 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale15 D C PRO 282 D PRO 282 1_555 D N MSE 283 D MSE 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.266 ? covale ? covale16 D C MSE 283 D MSE 283 1_555 D N ARG 284 D ARG 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.283 ? # _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 3VYW _atom_sites.fract_transf_matrix[1][1] 0.018022 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003976 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009295 _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] 0.0087 _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 E 2 SAM A 1 501 501 SAM SAM . F 2 SAM B 1 401 502 SAM SAM . G 3 BEN B 1 402 1001 BEN BEN . H 2 SAM C 1 401 503 SAM SAM . I 3 BEN C 1 402 1002 BEN BEN . J 2 SAM D 1 401 504 SAM SAM . K 4 HOH A 1 601 505 HOH HOH . K 4 HOH A 2 602 506 HOH HOH . K 4 HOH A 3 603 507 HOH HOH . K 4 HOH A 4 604 508 HOH HOH . K 4 HOH A 5 605 509 HOH HOH . K 4 HOH A 6 606 510 HOH HOH . K 4 HOH A 7 607 511 HOH HOH . K 4 HOH A 8 608 512 HOH HOH . K 4 HOH A 9 609 513 HOH HOH . K 4 HOH A 10 610 514 HOH HOH . K 4 HOH A 11 611 515 HOH HOH . K 4 HOH A 12 612 516 HOH HOH . K 4 HOH A 13 613 517 HOH HOH . K 4 HOH A 14 614 518 HOH HOH . K 4 HOH A 15 615 519 HOH HOH . K 4 HOH A 16 616 520 HOH HOH . K 4 HOH A 17 617 521 HOH HOH . K 4 HOH A 18 618 522 HOH HOH . K 4 HOH A 19 619 523 HOH HOH . K 4 HOH A 20 620 524 HOH HOH . K 4 HOH A 21 621 525 HOH HOH . K 4 HOH A 22 622 526 HOH HOH . K 4 HOH A 23 623 527 HOH HOH . K 4 HOH A 24 624 528 HOH HOH . K 4 HOH A 25 625 529 HOH HOH . K 4 HOH A 26 626 530 HOH HOH . K 4 HOH A 27 627 531 HOH HOH . K 4 HOH A 28 628 532 HOH HOH . K 4 HOH A 29 629 533 HOH HOH . K 4 HOH A 30 630 534 HOH HOH . K 4 HOH A 31 631 535 HOH HOH . K 4 HOH A 32 632 536 HOH HOH . K 4 HOH A 33 633 537 HOH HOH . K 4 HOH A 34 634 538 HOH HOH . K 4 HOH A 35 635 539 HOH HOH . K 4 HOH A 36 636 540 HOH HOH . K 4 HOH A 37 637 541 HOH HOH . K 4 HOH A 38 638 542 HOH HOH . K 4 HOH A 39 639 543 HOH HOH . K 4 HOH A 40 640 544 HOH HOH . K 4 HOH A 41 641 545 HOH HOH . K 4 HOH A 42 642 546 HOH HOH . L 4 HOH B 1 501 1003 HOH HOH . L 4 HOH B 2 502 1004 HOH HOH . L 4 HOH B 3 503 1005 HOH HOH . L 4 HOH B 4 504 1006 HOH HOH . L 4 HOH B 5 505 1007 HOH HOH . L 4 HOH B 6 506 1008 HOH HOH . L 4 HOH B 7 507 1009 HOH HOH . L 4 HOH B 8 508 1010 HOH HOH . L 4 HOH B 9 509 1011 HOH HOH . L 4 HOH B 10 510 1012 HOH HOH . L 4 HOH B 11 511 1013 HOH HOH . L 4 HOH B 12 512 1014 HOH HOH . L 4 HOH B 13 513 1015 HOH HOH . L 4 HOH B 14 514 1016 HOH HOH . L 4 HOH B 15 515 1017 HOH HOH . L 4 HOH B 16 516 1018 HOH HOH . L 4 HOH B 17 517 1019 HOH HOH . L 4 HOH B 18 518 1020 HOH HOH . L 4 HOH B 19 519 1021 HOH HOH . L 4 HOH B 20 520 1022 HOH HOH . L 4 HOH B 21 521 1023 HOH HOH . L 4 HOH B 22 522 1024 HOH HOH . L 4 HOH B 23 523 1025 HOH HOH . L 4 HOH B 24 524 1026 HOH HOH . L 4 HOH B 25 525 1027 HOH HOH . L 4 HOH B 26 526 1028 HOH HOH . L 4 HOH B 27 527 1029 HOH HOH . L 4 HOH B 28 528 1030 HOH HOH . L 4 HOH B 29 529 1031 HOH HOH . L 4 HOH B 30 530 1032 HOH HOH . L 4 HOH B 31 531 1033 HOH HOH . L 4 HOH B 32 532 1034 HOH HOH . M 4 HOH C 1 501 1003 HOH HOH . M 4 HOH C 2 502 1004 HOH HOH . M 4 HOH C 3 503 1005 HOH HOH . M 4 HOH C 4 504 1006 HOH HOH . M 4 HOH C 5 505 1007 HOH HOH . M 4 HOH C 6 506 1008 HOH HOH . M 4 HOH C 7 507 1009 HOH HOH . M 4 HOH C 8 508 1010 HOH HOH . M 4 HOH C 9 509 1011 HOH HOH . M 4 HOH C 10 510 1012 HOH HOH . M 4 HOH C 11 511 1013 HOH HOH . M 4 HOH C 12 512 1014 HOH HOH . M 4 HOH C 13 513 1015 HOH HOH . M 4 HOH C 14 514 1016 HOH HOH . M 4 HOH C 15 515 1017 HOH HOH . M 4 HOH C 16 516 1018 HOH HOH . M 4 HOH C 17 517 1019 HOH HOH . M 4 HOH C 18 518 1020 HOH HOH . M 4 HOH C 19 519 1021 HOH HOH . M 4 HOH C 20 520 1022 HOH HOH . M 4 HOH C 21 521 1023 HOH HOH . M 4 HOH C 22 522 1024 HOH HOH . M 4 HOH C 23 523 1025 HOH HOH . M 4 HOH C 24 524 1026 HOH HOH . M 4 HOH C 25 525 1027 HOH HOH . M 4 HOH C 26 526 1028 HOH HOH . M 4 HOH C 27 527 1029 HOH HOH . M 4 HOH C 28 528 1030 HOH HOH . M 4 HOH C 29 529 1031 HOH HOH . M 4 HOH C 30 530 1032 HOH HOH . M 4 HOH C 31 531 1033 HOH HOH . M 4 HOH C 32 532 1034 HOH HOH . M 4 HOH C 33 533 1035 HOH HOH . M 4 HOH C 34 534 1036 HOH HOH . N 4 HOH D 1 501 505 HOH HOH . N 4 HOH D 2 502 506 HOH HOH . N 4 HOH D 3 503 507 HOH HOH . N 4 HOH D 4 504 508 HOH HOH . N 4 HOH D 5 505 509 HOH HOH . N 4 HOH D 6 506 510 HOH HOH . N 4 HOH D 7 507 511 HOH HOH . N 4 HOH D 8 508 512 HOH HOH . N 4 HOH D 9 509 513 HOH HOH . N 4 HOH D 10 510 514 HOH HOH . N 4 HOH D 11 511 515 HOH HOH . N 4 HOH D 12 512 516 HOH HOH . N 4 HOH D 13 513 517 HOH HOH . N 4 HOH D 14 514 518 HOH HOH . N 4 HOH D 15 515 519 HOH HOH . N 4 HOH D 16 516 520 HOH HOH . N 4 HOH D 17 517 521 HOH HOH . N 4 HOH D 18 518 522 HOH HOH . N 4 HOH D 19 519 523 HOH HOH . N 4 HOH D 20 520 524 HOH HOH . N 4 HOH D 21 521 525 HOH HOH . N 4 HOH D 22 522 526 HOH HOH . N 4 HOH D 23 523 527 HOH HOH . N 4 HOH D 24 524 528 HOH HOH . N 4 HOH D 25 525 529 HOH HOH . N 4 HOH D 26 526 530 HOH HOH . N 4 HOH D 27 527 531 HOH HOH . N 4 HOH D 28 528 532 HOH HOH . N 4 HOH D 29 529 533 HOH HOH . N 4 HOH D 30 530 534 HOH HOH . N 4 HOH D 31 531 535 HOH HOH . N 4 HOH D 32 532 536 HOH HOH . N 4 HOH D 33 533 537 HOH HOH . N 4 HOH D 34 534 538 HOH HOH . N 4 HOH D 35 535 539 HOH HOH . N 4 HOH D 36 536 540 HOH HOH . N 4 HOH D 37 537 541 HOH HOH . N 4 HOH D 38 538 542 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 . . . I 3 -30.174 36.601 -19.457 1 48.75 ? C1 BEN 402 C 1 HETATM 2 C C2 BEN . . . I 3 -28.935 37.234 -19.442 1 44.03 ? C2 BEN 402 C 1 HETATM 3 C C3 BEN . . . I 3 -28.695 38.277 -20.37 1 41.88 ? C3 BEN 402 C 1 HETATM 4 C C4 BEN . . . I 3 -29.644 38.672 -21.324 1 39.07 ? C4 BEN 402 C 1 HETATM 5 C C5 BEN . . . I 3 -30.875 38.014 -21.332 1 41.39 ? C5 BEN 402 C 1 HETATM 6 C C6 BEN . . . I 3 -31.129 37.002 -20.402 1 45.49 ? C6 BEN 402 C 1 HETATM 7 C C BEN . . . I 3 -30.482 35.516 -18.477 1 54.94 ? C BEN 402 C 1 HETATM 8 N N1 BEN . . . I 3 -31.65 34.858 -18.539 1 54.9 ? N1 BEN 402 C 1 HETATM 9 N N2 BEN . . . I 3 -29.623 35.249 -17.58 1 70.26 ? N2 BEN 402 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 9 #