data_1D7S # _model_server_result.job_id WUY6BkHRVpJezXL8ZS3IFg _model_server_result.datetime_utc '2025-02-27 01:13:23' _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 1d7s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 1D7S # _exptl.entry_id 1D7S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 333.234 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE _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 1D7S _cell.length_a 152.88 _cell.length_b 152.88 _cell.length_c 86.36 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D7S _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 76.44 132.397964 0 3 'crystal symmetry operation' 7_555 y,x,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 28.786667 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 76.44 132.397964 28.786667 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 metalc ? metalc1 A O LEU 78 A LEU 78 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc2 A OG SER 80 A SER 80 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc3 A O ALA 95 A ALA 95 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc4 A O THR 98 A THR 98 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc5 A OG1 THR 98 A THR 98 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.983 ? metalc ? metalc6 A O PRO 99 A PRO 99 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc7 A O LEU 102 A LEU 102 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc8 A O THR 303 A THR 303 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? metalc ? metalc9 A O VAL 305 A VAL 305 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc10 A OD1 ASP 307 A ASP 307 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc11 C K K . A K 436 1_555 E O HOH . A HOH 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? # _chem_comp.formula 'C11 H16 N3 O7 P' _chem_comp.formula_weight 333.234 _chem_comp.id DCS _chem_comp.mon_nstd_flag . _chem_comp.name D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE # 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 N1 C2 DCS doub 83 n y N1 C6 DCS sing 84 n y C2 C2A DCS sing 85 n n C2 C3 DCS sing 86 n y C2A H2A1 DCS sing 87 n n C2A H2A2 DCS sing 88 n n C2A H2A3 DCS sing 89 n n C3 O3 DCS sing 90 n n C3 C4 DCS doub 91 n y O3 HO3 DCS sing 92 n n C4 C4A DCS sing 93 n n C4 C5 DCS sing 94 n y C4A N DCS sing 95 n n C4A H4A1 DCS sing 96 n n C4A H4A2 DCS sing 97 n n C5 C6 DCS doub 98 n y C5 C5A DCS sing 99 n n C6 H6 DCS sing 100 n n C5A O4P DCS sing 101 n n C5A H5A1 DCS sing 102 n n C5A H5A2 DCS sing 103 n n O4P P DCS sing 104 n n P O1P DCS doub 105 n n P O2P DCS sing 106 n n P O3P DCS sing 107 n n O2P HOP2 DCS sing 108 n n O3P HOP3 DCS sing 109 n n N CA DCS sing 110 n n N HN DCS sing 111 n n CA C DCS sing 112 n n CA CB DCS sing 113 n n CA HA DCS sing 114 n n C O DCS doub 115 n n C ND DCS sing 116 n n ND OG DCS sing 117 n n ND HND DCS sing 118 n n OG CB DCS sing 119 n n CB HB1 DCS sing 120 n n CB HB2 DCS sing 121 n n # _atom_sites.entry_id 1D7S _atom_sites.fract_transf_matrix[1][1] 0.006541 _atom_sites.fract_transf_matrix[1][2] 0.003776 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007553 _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] 0.011579 _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 NA A 1 435 435 NA NA+ . C 3 K A 1 436 436 K K+ . D 4 DCS A 1 500 500 DCS DCS . E 5 HOH A 1 501 501 HOH WAT . E 5 HOH A 2 502 502 HOH WAT . E 5 HOH A 3 503 503 HOH WAT . E 5 HOH A 4 504 504 HOH WAT . E 5 HOH A 5 505 505 HOH WAT . E 5 HOH A 6 506 506 HOH WAT . E 5 HOH A 7 507 507 HOH WAT . E 5 HOH A 8 508 508 HOH WAT . E 5 HOH A 9 509 509 HOH WAT . E 5 HOH A 10 510 510 HOH WAT . E 5 HOH A 11 511 511 HOH WAT . E 5 HOH A 12 512 512 HOH WAT . E 5 HOH A 13 513 513 HOH WAT . E 5 HOH A 14 514 514 HOH WAT . E 5 HOH A 15 515 515 HOH WAT . E 5 HOH A 16 516 516 HOH WAT . E 5 HOH A 17 517 517 HOH WAT . E 5 HOH A 18 518 518 HOH WAT . E 5 HOH A 19 519 519 HOH WAT . E 5 HOH A 20 520 520 HOH WAT . E 5 HOH A 21 521 521 HOH WAT . E 5 HOH A 22 522 522 HOH WAT . E 5 HOH A 23 523 523 HOH WAT . E 5 HOH A 24 524 524 HOH WAT . E 5 HOH A 25 525 525 HOH WAT . E 5 HOH A 26 526 526 HOH WAT . E 5 HOH A 27 527 527 HOH WAT . E 5 HOH A 28 528 528 HOH WAT . E 5 HOH A 29 529 529 HOH WAT . E 5 HOH A 30 530 530 HOH WAT . E 5 HOH A 31 531 531 HOH WAT . E 5 HOH A 32 532 532 HOH WAT . E 5 HOH A 33 533 533 HOH WAT . E 5 HOH A 34 534 534 HOH WAT . E 5 HOH A 35 535 535 HOH WAT . E 5 HOH A 36 536 536 HOH WAT . E 5 HOH A 37 537 537 HOH WAT . E 5 HOH A 38 538 538 HOH WAT . E 5 HOH A 39 540 540 HOH WAT . E 5 HOH A 40 541 541 HOH WAT . E 5 HOH A 41 542 542 HOH WAT . E 5 HOH A 42 543 543 HOH WAT . E 5 HOH A 43 544 544 HOH WAT . E 5 HOH A 44 545 545 HOH WAT . E 5 HOH A 45 546 546 HOH WAT . E 5 HOH A 46 547 547 HOH WAT . E 5 HOH A 47 548 548 HOH WAT . E 5 HOH A 48 549 549 HOH WAT . E 5 HOH A 49 550 550 HOH WAT . E 5 HOH A 50 551 551 HOH WAT . E 5 HOH A 51 552 552 HOH WAT . E 5 HOH A 52 553 553 HOH WAT . E 5 HOH A 53 554 554 HOH WAT . E 5 HOH A 54 555 555 HOH WAT . E 5 HOH A 55 556 556 HOH WAT . E 5 HOH A 56 557 557 HOH WAT . E 5 HOH A 57 558 558 HOH WAT . E 5 HOH A 58 559 559 HOH WAT . E 5 HOH A 59 560 560 HOH WAT . E 5 HOH A 60 561 561 HOH WAT . E 5 HOH A 61 562 562 HOH WAT . E 5 HOH A 62 563 563 HOH WAT . E 5 HOH A 63 564 564 HOH WAT . E 5 HOH A 64 565 565 HOH WAT . E 5 HOH A 65 566 566 HOH WAT . E 5 HOH A 66 568 568 HOH WAT . E 5 HOH A 67 569 569 HOH WAT . E 5 HOH A 68 570 570 HOH WAT . E 5 HOH A 69 571 571 HOH WAT . E 5 HOH A 70 572 572 HOH WAT . E 5 HOH A 71 573 573 HOH WAT . E 5 HOH A 72 574 574 HOH WAT . E 5 HOH A 73 575 575 HOH WAT . E 5 HOH A 74 576 576 HOH WAT . E 5 HOH A 75 577 577 HOH WAT . E 5 HOH A 76 578 578 HOH WAT . E 5 HOH A 77 580 580 HOH WAT . E 5 HOH A 78 581 581 HOH WAT . E 5 HOH A 79 582 582 HOH WAT . E 5 HOH A 80 583 583 HOH WAT . E 5 HOH A 81 584 584 HOH WAT . E 5 HOH A 82 585 585 HOH WAT . E 5 HOH A 83 586 586 HOH WAT . E 5 HOH A 84 587 587 HOH WAT . E 5 HOH A 85 588 588 HOH WAT . E 5 HOH A 86 589 589 HOH WAT . E 5 HOH A 87 590 590 HOH WAT . E 5 HOH A 88 591 591 HOH WAT . E 5 HOH A 89 601 601 HOH WAT . E 5 HOH A 90 602 602 HOH WAT . E 5 HOH A 91 603 603 HOH WAT . E 5 HOH A 92 604 604 HOH WAT . E 5 HOH A 93 605 605 HOH WAT . E 5 HOH A 94 606 606 HOH WAT . E 5 HOH A 95 607 607 HOH WAT . E 5 HOH A 96 608 608 HOH WAT . E 5 HOH A 97 609 609 HOH WAT . E 5 HOH A 98 610 610 HOH WAT . E 5 HOH A 99 611 611 HOH WAT . E 5 HOH A 100 612 612 HOH WAT . E 5 HOH A 101 613 613 HOH WAT . E 5 HOH A 102 614 614 HOH WAT . E 5 HOH A 103 615 615 HOH WAT . E 5 HOH A 104 616 616 HOH WAT . E 5 HOH A 105 617 617 HOH WAT . E 5 HOH A 106 618 618 HOH WAT . E 5 HOH A 107 619 619 HOH WAT . E 5 HOH A 108 622 622 HOH WAT . E 5 HOH A 109 627 627 HOH WAT . E 5 HOH A 110 628 628 HOH WAT . E 5 HOH A 111 629 629 HOH WAT . E 5 HOH A 112 630 630 HOH WAT . E 5 HOH A 113 631 631 HOH WAT . E 5 HOH A 114 632 632 HOH WAT . E 5 HOH A 115 633 633 HOH WAT . E 5 HOH A 116 635 635 HOH WAT . E 5 HOH A 117 636 636 HOH WAT . E 5 HOH A 118 638 638 HOH WAT . E 5 HOH A 119 639 639 HOH WAT . E 5 HOH A 120 641 641 HOH WAT . E 5 HOH A 121 642 642 HOH WAT . E 5 HOH A 122 643 643 HOH WAT . E 5 HOH A 123 644 644 HOH WAT . E 5 HOH A 124 645 645 HOH WAT . E 5 HOH A 125 646 646 HOH WAT . E 5 HOH A 126 648 648 HOH WAT . E 5 HOH A 127 650 650 HOH WAT . E 5 HOH A 128 652 652 HOH WAT . E 5 HOH A 129 661 661 HOH WAT . E 5 HOH A 130 662 662 HOH WAT . E 5 HOH A 131 663 663 HOH WAT . E 5 HOH A 132 664 664 HOH WAT . E 5 HOH A 133 665 665 HOH WAT . E 5 HOH A 134 666 666 HOH WAT . E 5 HOH A 135 667 667 HOH WAT . E 5 HOH A 136 670 670 HOH WAT . E 5 HOH A 137 671 671 HOH WAT . E 5 HOH A 138 674 674 HOH WAT . E 5 HOH A 139 675 675 HOH WAT . E 5 HOH A 140 676 676 HOH WAT . E 5 HOH A 141 677 677 HOH WAT . E 5 HOH A 142 679 679 HOH WAT . E 5 HOH A 143 680 680 HOH WAT . # 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 N1 DCS . . . D 4 17.453 53.482 13.804 1 27.11 ? N1 DCS 500 A 1 HETATM 2 C C2 DCS . . . D 4 16.379 53.724 14.6 1 21.45 ? C2 DCS 500 A 1 HETATM 3 C C2A DCS . . . D 4 15.295 54.664 14.153 1 25.67 ? C2A DCS 500 A 1 HETATM 4 C C3 DCS . . . D 4 16.366 53.125 15.872 1 29.15 ? C3 DCS 500 A 1 HETATM 5 O O3 DCS . . . D 4 15.3 53.461 16.621 1 25.23 ? O3 DCS 500 A 1 HETATM 6 C C4 DCS . . . D 4 17.409 52.303 16.296 1 29.21 ? C4 DCS 500 A 1 HETATM 7 C C4A DCS . . . D 4 17.439 51.643 17.599 1 41.71 ? C4A DCS 500 A 1 HETATM 8 C C5 DCS . . . D 4 18.452 52.06 15.368 1 30.27 ? C5 DCS 500 A 1 HETATM 9 C C6 DCS . . . D 4 18.475 52.654 14.146 1 25.71 ? C6 DCS 500 A 1 HETATM 10 C C5A DCS . . . D 4 19.644 51.169 15.818 1 21.67 ? C5A DCS 500 A 1 HETATM 11 O O4P DCS . . . D 4 19.332 49.771 15.88 1 32.55 ? O4P DCS 500 A 1 HETATM 12 P P DCS . . . D 4 20.233 48.741 16.735 1 26.98 ? P DCS 500 A 1 HETATM 13 O O1P DCS . . . D 4 20.077 49.119 18.148 1 38.1 ? O1P DCS 500 A 1 HETATM 14 O O2P DCS . . . D 4 19.704 47.32 16.453 1 31.97 ? O2P DCS 500 A 1 HETATM 15 O O3P DCS . . . D 4 21.588 48.863 16.198 1 23.1 ? O3P DCS 500 A 1 HETATM 16 N N DCS . . . D 4 16.4 51.583 18.38 1 32.15 ? N DCS 500 A 1 HETATM 17 C CA DCS . . . D 4 16.435 51.972 19.667 1 100 ? CA DCS 500 A 1 HETATM 18 C C DCS . . . D 4 15.241 51.886 20.374 1 70.81 ? C DCS 500 A 1 HETATM 19 O O DCS . . . D 4 14.067 52.401 20.322 1 39.81 ? O DCS 500 A 1 HETATM 20 N ND DCS . . . D 4 15.422 51.083 21.375 1 100 ? ND DCS 500 A 1 HETATM 21 O OG DCS . . . D 4 16.765 50.604 21.312 1 100 ? OG DCS 500 A 1 HETATM 22 C CB DCS . . . D 4 17.405 51.175 20.255 1 100 ? CB DCS 500 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 22 #