data_6D5O # _model_server_result.job_id W7nzO_zdnL-ky15KmyJv5A _model_server_result.datetime_utc '2024-11-26 20:52:41' _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 6d5o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6D5O # _exptl.entry_id 6D5O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 117.146 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description VALINE _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 120 _cell.entry_id 6D5O _cell.length_a 93.931 _cell.length_b 93.931 _cell.length_c 131.656 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6D5O _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall 'P 61 2 (x,y,z+5/12)' _symmetry.space_group_name_H-M 'P 61 2 2' # _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,H,I,J,K,L,M _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 2 _struct_asym.id B _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 covale ? covale1 B C VAL . A VAL 401 1_555 C N LYS . A LYS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 sing metalc ? metalc1 A OD1 ASP 57 A ASP 57 1_555 F CA CA . A CA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc2 A OD2 ASP 57 A ASP 57 1_555 F CA CA . A CA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc3 A OD1 ASP 59 A ASP 59 1_555 F CA CA . A CA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc4 A O GLN 61 A GLN 61 1_555 F CA CA . A CA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc5 A OD2 ASP 138 A ASP 138 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc6 A NE2 HIS 142 A HIS 142 1_555 D ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc7 A NE2 HIS 146 A HIS 146 1_555 D ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc8 A OE1 GLU 166 A GLU 166 1_555 D ZN ZN . A ZN 403 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc9 A OE2 GLU 166 A GLU 166 1_555 D ZN ZN . A ZN 403 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.867 ? metalc ? metalc10 A OE1 GLU 177 A GLU 177 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc11 A OE2 GLU 177 A GLU 177 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc12 A OE2 GLU 177 A GLU 177 1_555 H CA CA . A CA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc13 A O ASN 183 A ASN 183 1_555 H CA CA . A CA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc14 A OD1 ASP 185 A ASP 185 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc15 A OD2 ASP 185 A ASP 185 1_555 H CA CA . A CA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc16 A O GLU 187 A GLU 187 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc17 A OE1 GLU 190 A GLU 190 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc18 A OE2 GLU 190 A GLU 190 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc19 A OE2 GLU 190 A GLU 190 1_555 H CA CA . A CA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc20 A O TYR 193 A TYR 193 1_555 G CA CA . A CA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc21 A O THR 194 A THR 194 1_555 G CA CA . A CA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc22 A OG1 THR 194 A THR 194 1_555 G CA CA . A CA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc23 A O ILE 197 A ILE 197 1_555 G CA CA . A CA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc24 A OD1 ASP 200 A ASP 200 1_555 G CA CA . A CA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc25 D ZN ZN . A ZN 403 1_555 M O HOH . A HOH 503 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.648 ? metalc ? metalc26 D ZN ZN . A ZN 403 1_555 M O HOH . A HOH 508 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.86 ? metalc ? metalc27 E CA CA . A CA 404 1_555 M O HOH . A HOH 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc28 F CA CA . A CA 405 1_555 M O HOH . A HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc29 F CA CA . A CA 405 1_555 M O HOH . A HOH 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc30 F CA CA . A CA 405 1_555 M O HOH . A HOH 627 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc31 G CA CA . A CA 406 1_555 M O HOH . A HOH 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc32 G CA CA . A CA 406 1_555 M O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc33 H CA CA . A CA 407 1_555 M O HOH . A HOH 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc34 H CA CA . A CA 407 1_555 M O HOH . A HOH 571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? # _chem_comp.formula 'C5 H11 N O2' _chem_comp.formula_weight 117.146 _chem_comp.id VAL _chem_comp.mon_nstd_flag y _chem_comp.name VALINE _chem_comp.type 'l-peptide linking' _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 N CA VAL sing 356 n n N H VAL sing 357 n n N H2 VAL sing 358 n n CA C VAL sing 359 n n CA CB VAL sing 360 n n CA HA VAL sing 361 n n C O VAL doub 362 n n C OXT VAL sing 363 n n CB CG1 VAL sing 364 n n CB CG2 VAL sing 365 n n CB HB VAL sing 366 n n CG1 HG11 VAL sing 367 n n CG1 HG12 VAL sing 368 n n CG1 HG13 VAL sing 369 n n CG2 HG21 VAL sing 370 n n CG2 HG22 VAL sing 371 n n CG2 HG23 VAL sing 372 n n OXT HXT VAL sing 373 n n # _atom_sites.entry_id 6D5O _atom_sites.fract_transf_matrix[1][1] 0.010646 _atom_sites.fract_transf_matrix[1][2] 0.006147 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012293 _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] 0.007596 _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 VAL A 1 401 1322 VAL VAL . C 3 LYS A 1 402 1323 LYS LYS . D 4 ZN A 1 403 1 ZN ZN . E 5 CA A 1 404 1 CA CA . F 5 CA A 1 405 2 CA CA . G 5 CA A 1 406 3 CA CA . H 5 CA A 1 407 4 CA CA . I 6 DMF A 1 408 1 DMF DMF . J 6 DMF A 1 409 2 DMF DMF . K 6 DMF A 1 410 3 DMF DMF . L 6 DMF A 1 411 4 DMF DMF . M 7 HOH A 1 501 107 HOH HOH . M 7 HOH A 2 502 106 HOH HOH . M 7 HOH A 3 503 137 HOH HOH . M 7 HOH A 4 504 99 HOH HOH . M 7 HOH A 5 505 120 HOH HOH . M 7 HOH A 6 506 86 HOH HOH . M 7 HOH A 7 507 103 HOH HOH . M 7 HOH A 8 508 84 HOH HOH . M 7 HOH A 9 509 104 HOH HOH . M 7 HOH A 10 510 64 HOH HOH . M 7 HOH A 11 511 20 HOH HOH . M 7 HOH A 12 512 14 HOH HOH . M 7 HOH A 13 513 19 HOH HOH . M 7 HOH A 14 514 10 HOH HOH . M 7 HOH A 15 515 18 HOH HOH . M 7 HOH A 16 516 121 HOH HOH . M 7 HOH A 17 517 12 HOH HOH . M 7 HOH A 18 518 97 HOH HOH . M 7 HOH A 19 519 29 HOH HOH . M 7 HOH A 20 520 11 HOH HOH . M 7 HOH A 21 521 66 HOH HOH . M 7 HOH A 22 522 17 HOH HOH . M 7 HOH A 23 523 7 HOH HOH . M 7 HOH A 24 524 95 HOH HOH . M 7 HOH A 25 525 109 HOH HOH . M 7 HOH A 26 526 52 HOH HOH . M 7 HOH A 27 527 71 HOH HOH . M 7 HOH A 28 528 45 HOH HOH . M 7 HOH A 29 529 98 HOH HOH . M 7 HOH A 30 530 59 HOH HOH . M 7 HOH A 31 531 102 HOH HOH . M 7 HOH A 32 532 47 HOH HOH . M 7 HOH A 33 533 74 HOH HOH . M 7 HOH A 34 534 33 HOH HOH . M 7 HOH A 35 535 5 HOH HOH . M 7 HOH A 36 536 85 HOH HOH . M 7 HOH A 37 537 36 HOH HOH . M 7 HOH A 38 538 82 HOH HOH . M 7 HOH A 39 539 49 HOH HOH . M 7 HOH A 40 540 58 HOH HOH . M 7 HOH A 41 541 6 HOH HOH . M 7 HOH A 42 542 67 HOH HOH . M 7 HOH A 43 543 4 HOH HOH . M 7 HOH A 44 544 24 HOH HOH . M 7 HOH A 45 545 130 HOH HOH . M 7 HOH A 46 546 72 HOH HOH . M 7 HOH A 47 547 77 HOH HOH . M 7 HOH A 48 548 43 HOH HOH . M 7 HOH A 49 549 1 HOH HOH . M 7 HOH A 50 550 124 HOH HOH . M 7 HOH A 51 551 65 HOH HOH . M 7 HOH A 52 552 23 HOH HOH . M 7 HOH A 53 553 34 HOH HOH . M 7 HOH A 54 554 56 HOH HOH . M 7 HOH A 55 555 129 HOH HOH . M 7 HOH A 56 556 132 HOH HOH . M 7 HOH A 57 557 31 HOH HOH . M 7 HOH A 58 558 37 HOH HOH . M 7 HOH A 59 559 91 HOH HOH . M 7 HOH A 60 560 42 HOH HOH . M 7 HOH A 61 561 127 HOH HOH . M 7 HOH A 62 562 110 HOH HOH . M 7 HOH A 63 563 116 HOH HOH . M 7 HOH A 64 564 46 HOH HOH . M 7 HOH A 65 565 69 HOH HOH . M 7 HOH A 66 566 9 HOH HOH . M 7 HOH A 67 567 40 HOH HOH . M 7 HOH A 68 568 75 HOH HOH . M 7 HOH A 69 569 113 HOH HOH . M 7 HOH A 70 570 50 HOH HOH . M 7 HOH A 71 571 3 HOH HOH . M 7 HOH A 72 572 126 HOH HOH . M 7 HOH A 73 573 8 HOH HOH . M 7 HOH A 74 574 133 HOH HOH . M 7 HOH A 75 575 22 HOH HOH . M 7 HOH A 76 576 16 HOH HOH . M 7 HOH A 77 577 60 HOH HOH . M 7 HOH A 78 578 108 HOH HOH . M 7 HOH A 79 579 21 HOH HOH . M 7 HOH A 80 580 92 HOH HOH . M 7 HOH A 81 581 68 HOH HOH . M 7 HOH A 82 582 114 HOH HOH . M 7 HOH A 83 583 35 HOH HOH . M 7 HOH A 84 584 94 HOH HOH . M 7 HOH A 85 585 25 HOH HOH . M 7 HOH A 86 586 13 HOH HOH . M 7 HOH A 87 587 62 HOH HOH . M 7 HOH A 88 588 88 HOH HOH . M 7 HOH A 89 589 90 HOH HOH . M 7 HOH A 90 590 2 HOH HOH . M 7 HOH A 91 591 28 HOH HOH . M 7 HOH A 92 592 54 HOH HOH . M 7 HOH A 93 593 41 HOH HOH . M 7 HOH A 94 594 26 HOH HOH . M 7 HOH A 95 595 39 HOH HOH . M 7 HOH A 96 596 55 HOH HOH . M 7 HOH A 97 597 93 HOH HOH . M 7 HOH A 98 598 38 HOH HOH . M 7 HOH A 99 599 89 HOH HOH . M 7 HOH A 100 600 48 HOH HOH . M 7 HOH A 101 601 30 HOH HOH . M 7 HOH A 102 602 27 HOH HOH . M 7 HOH A 103 603 135 HOH HOH . M 7 HOH A 104 604 123 HOH HOH . M 7 HOH A 105 605 96 HOH HOH . M 7 HOH A 106 606 32 HOH HOH . M 7 HOH A 107 607 15 HOH HOH . M 7 HOH A 108 608 100 HOH HOH . M 7 HOH A 109 609 80 HOH HOH . M 7 HOH A 110 610 87 HOH HOH . M 7 HOH A 111 611 51 HOH HOH . M 7 HOH A 112 612 112 HOH HOH . M 7 HOH A 113 613 136 HOH HOH . M 7 HOH A 114 614 44 HOH HOH . M 7 HOH A 115 615 78 HOH HOH . M 7 HOH A 116 616 138 HOH HOH . M 7 HOH A 117 617 111 HOH HOH . M 7 HOH A 118 618 131 HOH HOH . M 7 HOH A 119 619 73 HOH HOH . M 7 HOH A 120 620 81 HOH HOH . M 7 HOH A 121 621 57 HOH HOH . M 7 HOH A 122 622 139 HOH HOH . M 7 HOH A 123 623 53 HOH HOH . M 7 HOH A 124 624 70 HOH HOH . M 7 HOH A 125 625 122 HOH HOH . M 7 HOH A 126 626 76 HOH HOH . M 7 HOH A 127 627 83 HOH HOH . M 7 HOH A 128 628 125 HOH HOH . M 7 HOH A 129 629 115 HOH HOH . M 7 HOH A 130 630 134 HOH HOH . M 7 HOH A 131 631 128 HOH HOH . M 7 HOH A 132 632 61 HOH HOH . M 7 HOH A 133 633 63 HOH HOH . M 7 HOH A 134 634 101 HOH HOH . M 7 HOH A 135 635 105 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 N N VAL . . . B 2 11.649 -39.717 3.828 1 32.22 ? N VAL 401 A 1 HETATM 2 C CA VAL . . . B 2 10.454 -38.973 3.446 1 42.32 ? CA VAL 401 A 1 HETATM 3 C C VAL . . . B 2 9.199 -39.773 3.788 1 40.55 ? C VAL 401 A 1 HETATM 4 O O VAL . . . B 2 8.093 -39.235 3.766 1 26.21 ? O VAL 401 A 1 HETATM 5 C CB VAL . . . B 2 10.477 -38.61 1.948 1 26.24 ? CB VAL 401 A 1 HETATM 6 C CG1 VAL . . . B 2 10.225 -39.841 1.092 1 38.09 ? CG1 VAL 401 A 1 HETATM 7 C CG2 VAL . . . B 2 9.456 -37.513 1.645 1 28.73 ? CG2 VAL 401 A 1 HETATM 8 H HA VAL . . . B 2 10.426 -38.146 3.952 1 42.32 ? HA VAL 401 A 1 HETATM 9 H HB VAL . . . B 2 11.356 -38.267 1.723 1 26.24 ? HB VAL 401 A 1 HETATM 10 H HG11 VAL . . . B 2 10.245 -39.584 0.157 1 38.09 ? HG11 VAL 401 A 1 HETATM 11 H HG12 VAL . . . B 2 10.918 -40.496 1.27 1 38.09 ? HG12 VAL 401 A 1 HETATM 12 H HG13 VAL . . . B 2 9.356 -40.208 1.316 1 38.09 ? HG13 VAL 401 A 1 HETATM 13 H HG21 VAL . . . B 2 9.491 -37.303 0.699 1 28.73 ? HG21 VAL 401 A 1 HETATM 14 H HG22 VAL . . . B 2 8.571 -37.831 1.882 1 28.73 ? HG22 VAL 401 A 1 HETATM 15 H HG23 VAL . . . B 2 9.676 -36.725 2.167 1 28.73 ? HG23 VAL 401 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #