data_1VFS
#
_model_server_result.job_id            Dp0BDaJIyjpPABVW6izrbQ 
_model_server_result.datetime_utc      '2024-10-18 14:33:38' 
_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          1vfs 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1401}' 
#
_entry.id    1VFS 
#
_exptl.entry_id    1VFS 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              333.234 
_entity.id                          3 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          118.61 
_cell.angle_gamma         90 
_cell.entry_id            1VFS 
_cell.length_a            82.96 
_cell.length_b            63.55 
_cell.length_c            84.62 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1VFS 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 E 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 LEU 128 A LEU 128 1_555 A N KCX 129 A KCX 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale2 A C KCX 129 A KCX 129 1_555 A N ALA 130 A ALA 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale3 B C LEU 128 B LEU 1128 1_555 B N KCX 129 B KCX 1129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale4 B C KCX 129 B KCX 1129 1_555 B N ALA 130 B ALA 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
#
_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                     1VFS 
_atom_sites.fract_transf_matrix[1][1]    0.012054 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.006575 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015736 
_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]    0.013461 
_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
C 2 CL A 1 656 656 CL CL . 
D 3 DCS A 1 401 401 DCS SCP . 
E 3 DCS B 1 1401 1401 DCS SCP . 
F 4 HOH A 1 501 501 HOH HOH . 
F 4 HOH A 2 506 506 HOH HOH . 
F 4 HOH A 3 508 508 HOH HOH . 
F 4 HOH A 4 509 509 HOH HOH . 
F 4 HOH A 5 510 510 HOH HOH . 
F 4 HOH A 6 511 511 HOH HOH . 
F 4 HOH A 7 513 513 HOH HOH . 
F 4 HOH A 8 515 515 HOH HOH . 
F 4 HOH A 9 516 516 HOH HOH . 
F 4 HOH A 10 517 517 HOH HOH . 
F 4 HOH A 11 518 518 HOH HOH . 
F 4 HOH A 12 520 520 HOH HOH . 
F 4 HOH A 13 521 521 HOH HOH . 
F 4 HOH A 14 524 524 HOH HOH . 
F 4 HOH A 15 525 525 HOH HOH . 
F 4 HOH A 16 528 528 HOH HOH . 
F 4 HOH A 17 529 529 HOH HOH . 
F 4 HOH A 18 532 532 HOH HOH . 
F 4 HOH A 19 533 533 HOH HOH . 
F 4 HOH A 20 534 534 HOH HOH . 
F 4 HOH A 21 541 541 HOH HOH . 
F 4 HOH A 22 547 547 HOH HOH . 
F 4 HOH A 23 549 549 HOH HOH . 
F 4 HOH A 24 550 550 HOH HOH . 
F 4 HOH A 25 551 551 HOH HOH . 
F 4 HOH A 26 553 553 HOH HOH . 
F 4 HOH A 27 556 556 HOH HOH . 
F 4 HOH A 28 557 557 HOH HOH . 
F 4 HOH A 29 558 558 HOH HOH . 
F 4 HOH A 30 559 559 HOH HOH . 
F 4 HOH A 31 560 560 HOH HOH . 
F 4 HOH A 32 563 563 HOH HOH . 
F 4 HOH A 33 566 566 HOH HOH . 
F 4 HOH A 34 568 568 HOH HOH . 
F 4 HOH A 35 569 569 HOH HOH . 
F 4 HOH A 36 571 571 HOH HOH . 
F 4 HOH A 37 574 574 HOH HOH . 
F 4 HOH A 38 578 578 HOH HOH . 
F 4 HOH A 39 579 579 HOH HOH . 
F 4 HOH A 40 580 580 HOH HOH . 
F 4 HOH A 41 583 583 HOH HOH . 
F 4 HOH A 42 584 584 HOH HOH . 
F 4 HOH A 43 585 585 HOH HOH . 
F 4 HOH A 44 591 591 HOH HOH . 
F 4 HOH A 45 592 592 HOH HOH . 
F 4 HOH A 46 593 593 HOH HOH . 
F 4 HOH A 47 594 594 HOH HOH . 
F 4 HOH A 48 595 595 HOH HOH . 
F 4 HOH A 49 597 597 HOH HOH . 
F 4 HOH A 50 600 600 HOH HOH . 
F 4 HOH A 51 602 602 HOH HOH . 
F 4 HOH A 52 603 603 HOH HOH . 
F 4 HOH A 53 605 605 HOH HOH . 
F 4 HOH A 54 606 606 HOH HOH . 
F 4 HOH A 55 610 610 HOH HOH . 
F 4 HOH A 56 613 613 HOH HOH . 
F 4 HOH A 57 615 615 HOH HOH . 
F 4 HOH A 58 618 618 HOH HOH . 
F 4 HOH A 59 619 619 HOH HOH . 
F 4 HOH A 60 621 621 HOH HOH . 
F 4 HOH A 61 623 623 HOH HOH . 
F 4 HOH A 62 626 626 HOH HOH . 
F 4 HOH A 63 629 629 HOH HOH . 
F 4 HOH A 64 630 630 HOH HOH . 
F 4 HOH A 65 631 631 HOH HOH . 
F 4 HOH A 66 634 634 HOH HOH . 
F 4 HOH A 67 636 636 HOH HOH . 
F 4 HOH A 68 637 637 HOH HOH . 
F 4 HOH A 69 638 638 HOH HOH . 
F 4 HOH A 70 641 641 HOH HOH . 
F 4 HOH A 71 643 643 HOH HOH . 
F 4 HOH A 72 645 645 HOH HOH . 
F 4 HOH A 73 651 651 HOH HOH . 
F 4 HOH A 74 653 653 HOH HOH . 
F 4 HOH A 75 657 657 HOH HOH . 
G 4 HOH B 1 502 502 HOH HOH . 
G 4 HOH B 2 503 503 HOH HOH . 
G 4 HOH B 3 504 504 HOH HOH . 
G 4 HOH B 4 505 505 HOH HOH . 
G 4 HOH B 5 507 507 HOH HOH . 
G 4 HOH B 6 512 512 HOH HOH . 
G 4 HOH B 7 514 514 HOH HOH . 
G 4 HOH B 8 519 519 HOH HOH . 
G 4 HOH B 9 522 522 HOH HOH . 
G 4 HOH B 10 523 523 HOH HOH . 
G 4 HOH B 11 526 526 HOH HOH . 
G 4 HOH B 12 527 527 HOH HOH . 
G 4 HOH B 13 530 530 HOH HOH . 
G 4 HOH B 14 531 531 HOH HOH . 
G 4 HOH B 15 535 535 HOH HOH . 
G 4 HOH B 16 536 536 HOH HOH . 
G 4 HOH B 17 537 537 HOH HOH . 
G 4 HOH B 18 538 538 HOH HOH . 
G 4 HOH B 19 539 539 HOH HOH . 
G 4 HOH B 20 540 540 HOH HOH . 
G 4 HOH B 21 542 542 HOH HOH . 
G 4 HOH B 22 543 543 HOH HOH . 
G 4 HOH B 23 544 544 HOH HOH . 
G 4 HOH B 24 545 545 HOH HOH . 
G 4 HOH B 25 546 546 HOH HOH . 
G 4 HOH B 26 548 548 HOH HOH . 
G 4 HOH B 27 552 552 HOH HOH . 
G 4 HOH B 28 554 554 HOH HOH . 
G 4 HOH B 29 555 555 HOH HOH . 
G 4 HOH B 30 561 561 HOH HOH . 
G 4 HOH B 31 562 562 HOH HOH . 
G 4 HOH B 32 564 564 HOH HOH . 
G 4 HOH B 33 565 565 HOH HOH . 
G 4 HOH B 34 567 567 HOH HOH . 
G 4 HOH B 35 570 570 HOH HOH . 
G 4 HOH B 36 572 572 HOH HOH . 
G 4 HOH B 37 573 573 HOH HOH . 
G 4 HOH B 38 575 575 HOH HOH . 
G 4 HOH B 39 576 576 HOH HOH . 
G 4 HOH B 40 577 577 HOH HOH . 
G 4 HOH B 41 581 581 HOH HOH . 
G 4 HOH B 42 582 582 HOH HOH . 
G 4 HOH B 43 586 586 HOH HOH . 
G 4 HOH B 44 587 587 HOH HOH . 
G 4 HOH B 45 588 588 HOH HOH . 
G 4 HOH B 46 589 589 HOH HOH . 
G 4 HOH B 47 590 590 HOH HOH . 
G 4 HOH B 48 596 596 HOH HOH . 
G 4 HOH B 49 598 598 HOH HOH . 
G 4 HOH B 50 599 599 HOH HOH . 
G 4 HOH B 51 601 601 HOH HOH . 
G 4 HOH B 52 604 604 HOH HOH . 
G 4 HOH B 53 607 607 HOH HOH . 
G 4 HOH B 54 608 608 HOH HOH . 
G 4 HOH B 55 609 609 HOH HOH . 
G 4 HOH B 56 611 611 HOH HOH . 
G 4 HOH B 57 612 612 HOH HOH . 
G 4 HOH B 58 614 614 HOH HOH . 
G 4 HOH B 59 616 616 HOH HOH . 
G 4 HOH B 60 617 617 HOH HOH . 
G 4 HOH B 61 620 620 HOH HOH . 
G 4 HOH B 62 622 622 HOH HOH . 
G 4 HOH B 63 624 624 HOH HOH . 
G 4 HOH B 64 625 625 HOH HOH . 
G 4 HOH B 65 627 627 HOH HOH . 
G 4 HOH B 66 628 628 HOH HOH . 
G 4 HOH B 67 632 632 HOH HOH . 
G 4 HOH B 68 633 633 HOH HOH . 
G 4 HOH B 69 635 635 HOH HOH . 
G 4 HOH B 70 639 639 HOH HOH . 
G 4 HOH B 71 640 640 HOH HOH . 
G 4 HOH B 72 642 642 HOH HOH . 
G 4 HOH B 73 644 644 HOH HOH . 
G 4 HOH B 74 646 646 HOH HOH . 
G 4 HOH B 75 647 647 HOH HOH . 
G 4 HOH B 76 648 648 HOH HOH . 
G 4 HOH B 77 649 649 HOH HOH . 
G 4 HOH B 78 650 650 HOH HOH . 
G 4 HOH B 79 652 652 HOH HOH . 
G 4 HOH B 80 654 654 HOH HOH . 
G 4 HOH B 81 655 655 HOH HOH . 
G 4 HOH B 82 658 658 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 N1 DCS . . . E 3 11.972 1.112 -19.149 1 14.17 ? N1 DCS 1401 B 1 
HETATM 2 C C2 DCS . . . E 3 13.334 1.316 -18.872 1 19.92 ? C2 DCS 1401 B 1 
HETATM 3 C C2A DCS . . . E 3 14.395 1.125 -19.936 1 18.23 ? C2A DCS 1401 B 1 
HETATM 4 C C3 DCS . . . E 3 13.67 1.685 -17.594 1 22.47 ? C3 DCS 1401 B 1 
HETATM 5 O O3 DCS . . . E 3 14.949 1.936 -17.267 1 20.81 ? O3 DCS 1401 B 1 
HETATM 6 C C4 DCS . . . E 3 12.64 1.832 -16.624 1 25.19 ? C4 DCS 1401 B 1 
HETATM 7 C C4A DCS . . . E 3 12.992 2.179 -15.215 1 31.16 ? C4A DCS 1401 B 1 
HETATM 8 C C5 DCS . . . E 3 11.284 1.601 -17.007 1 16.73 ? C5 DCS 1401 B 1 
HETATM 9 C C6 DCS . . . E 3 10.988 1.25 -18.246 1 17.05 ? C6 DCS 1401 B 1 
HETATM 10 C C5A DCS . . . E 3 10.122 1.741 -16.04 1 14.4 ? C5A DCS 1401 B 1 
HETATM 11 O O4P DCS . . . E 3 9.946 3.108 -15.662 1 14.76 ? O4P DCS 1401 B 1 
HETATM 12 P P DCS . . . E 3 8.96 3.583 -14.51 1 18.83 ? P DCS 1401 B 1 
HETATM 13 O O1P DCS . . . E 3 7.632 3.105 -14.89 1 18.15 ? O1P DCS 1401 B 1 
HETATM 14 O O2P DCS . . . E 3 9.432 2.969 -13.269 1 15.07 ? O2P DCS 1401 B 1 
HETATM 15 O O3P DCS . . . E 3 9.028 5.04 -14.466 1 16.6 ? O3P DCS 1401 B 1 
HETATM 16 N N DCS . . . E 3 13.774 3.461 -15.179 1 36.72 ? N DCS 1401 B 1 
HETATM 17 C CA DCS . . . E 3 14.352 3.87 -13.979 1 39.19 ? CA DCS 1401 B 1 
HETATM 18 C C DCS . . . E 3 15.68 4.374 -13.872 1 39.13 ? C DCS 1401 B 1 
HETATM 19 O O DCS . . . E 3 16.667 4.187 -14.786 1 39.05 ? O DCS 1401 B 1 
HETATM 20 N ND DCS . . . E 3 15.791 5.048 -12.756 1 40.19 ? ND DCS 1401 B 1 
HETATM 21 O OG DCS . . . E 3 14.577 5.012 -12.105 1 42.33 ? OG DCS 1401 B 1 
HETATM 22 C CB DCS . . . E 3 13.706 4.297 -12.848 1 42.12 ? CB DCS 1401 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           22 
#