data_4LUT
#
_model_server_result.job_id            NtfhVu0wFb4TiFKlDSoYAA 
_model_server_result.datetime_utc      '2024-11-24 17:35:04' 
_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          4lut 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    4LUT 
#
_exptl.entry_id    4LUT 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            4LUT 
_cell.length_a            57.84 
_cell.length_b            138.97 
_cell.length_c            144.89 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4LUT 
_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        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 
_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 C N N 
? 3 D 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 B C VAL 129 B VAL 129 1_555 B N KCX 130 B KCX 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale2 B C KCX 130 B KCX 130 1_555 B N ILE 131 B ILE 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
#
_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                     4LUT 
_atom_sites.fract_transf_matrix[1][1]    0.017289 
_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]    0.007196 
_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]    0.006902 
_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 3 DCS A 1 401 401 DCS DCS . 
D 3 DCS B 1 401 401 DCS DCS . 
E 4 HOH A 1 501 501 HOH HOH . 
E 4 HOH A 2 502 502 HOH HOH . 
E 4 HOH A 3 503 503 HOH HOH . 
E 4 HOH A 4 504 504 HOH HOH . 
E 4 HOH A 5 505 505 HOH HOH . 
E 4 HOH A 6 506 506 HOH HOH . 
E 4 HOH A 7 507 507 HOH HOH . 
E 4 HOH A 8 508 508 HOH HOH . 
E 4 HOH A 9 509 509 HOH HOH . 
E 4 HOH A 10 510 510 HOH HOH . 
E 4 HOH A 11 511 511 HOH HOH . 
E 4 HOH A 12 512 513 HOH HOH . 
E 4 HOH A 13 513 514 HOH HOH . 
E 4 HOH A 14 514 515 HOH HOH . 
E 4 HOH A 15 515 516 HOH HOH . 
E 4 HOH A 16 516 518 HOH HOH . 
E 4 HOH A 17 517 519 HOH HOH . 
E 4 HOH A 18 518 522 HOH HOH . 
E 4 HOH A 19 519 523 HOH HOH . 
E 4 HOH A 20 520 524 HOH HOH . 
E 4 HOH A 21 521 525 HOH HOH . 
E 4 HOH A 22 522 526 HOH HOH . 
E 4 HOH A 23 523 527 HOH HOH . 
E 4 HOH A 24 524 528 HOH HOH . 
E 4 HOH A 25 525 529 HOH HOH . 
E 4 HOH A 26 526 530 HOH HOH . 
E 4 HOH A 27 527 531 HOH HOH . 
E 4 HOH A 28 528 532 HOH HOH . 
E 4 HOH A 29 529 533 HOH HOH . 
E 4 HOH A 30 530 534 HOH HOH . 
E 4 HOH A 31 531 536 HOH HOH . 
E 4 HOH A 32 532 538 HOH HOH . 
E 4 HOH A 33 533 539 HOH HOH . 
E 4 HOH A 34 534 540 HOH HOH . 
E 4 HOH A 35 535 541 HOH HOH . 
E 4 HOH A 36 536 542 HOH HOH . 
E 4 HOH A 37 537 543 HOH HOH . 
E 4 HOH A 38 538 544 HOH HOH . 
E 4 HOH A 39 539 546 HOH HOH . 
E 4 HOH A 40 540 547 HOH HOH . 
E 4 HOH A 41 541 548 HOH HOH . 
E 4 HOH A 42 542 549 HOH HOH . 
E 4 HOH A 43 543 550 HOH HOH . 
E 4 HOH A 44 544 551 HOH HOH . 
E 4 HOH A 45 545 552 HOH HOH . 
E 4 HOH A 46 546 553 HOH HOH . 
E 4 HOH A 47 547 554 HOH HOH . 
E 4 HOH A 48 548 555 HOH HOH . 
E 4 HOH A 49 549 556 HOH HOH . 
E 4 HOH A 50 550 557 HOH HOH . 
E 4 HOH A 51 551 558 HOH HOH . 
E 4 HOH A 52 552 559 HOH HOH . 
E 4 HOH A 53 553 560 HOH HOH . 
E 4 HOH A 54 554 562 HOH HOH . 
E 4 HOH A 55 555 563 HOH HOH . 
E 4 HOH A 56 556 565 HOH HOH . 
E 4 HOH A 57 557 566 HOH HOH . 
E 4 HOH A 58 558 567 HOH HOH . 
E 4 HOH A 59 559 568 HOH HOH . 
E 4 HOH A 60 560 569 HOH HOH . 
E 4 HOH A 61 561 570 HOH HOH . 
E 4 HOH A 62 562 571 HOH HOH . 
E 4 HOH A 63 563 572 HOH HOH . 
E 4 HOH A 64 564 574 HOH HOH . 
E 4 HOH A 65 565 576 HOH HOH . 
E 4 HOH A 66 566 580 HOH HOH . 
E 4 HOH A 67 567 581 HOH HOH . 
E 4 HOH A 68 568 582 HOH HOH . 
E 4 HOH A 69 569 583 HOH HOH . 
E 4 HOH A 70 570 584 HOH HOH . 
E 4 HOH A 71 571 585 HOH HOH . 
E 4 HOH A 72 572 586 HOH HOH . 
E 4 HOH A 73 573 587 HOH HOH . 
E 4 HOH A 74 574 589 HOH HOH . 
E 4 HOH A 75 575 590 HOH HOH . 
E 4 HOH A 76 576 592 HOH HOH . 
E 4 HOH A 77 577 593 HOH HOH . 
E 4 HOH A 78 578 594 HOH HOH . 
E 4 HOH A 79 579 595 HOH HOH . 
E 4 HOH A 80 580 596 HOH HOH . 
E 4 HOH A 81 581 597 HOH HOH . 
E 4 HOH A 82 582 577 HOH HOH . 
F 4 HOH B 1 501 520 HOH HOH . 
F 4 HOH B 2 502 521 HOH HOH . 
F 4 HOH B 3 503 535 HOH HOH . 
F 4 HOH B 4 504 579 HOH HOH . 
F 4 HOH B 5 505 501 HOH HOH . 
F 4 HOH B 6 506 502 HOH HOH . 
F 4 HOH B 7 507 503 HOH HOH . 
F 4 HOH B 8 508 504 HOH HOH . 
F 4 HOH B 9 509 505 HOH HOH . 
F 4 HOH B 10 510 506 HOH HOH . 
F 4 HOH B 11 511 507 HOH HOH . 
F 4 HOH B 12 512 508 HOH HOH . 
F 4 HOH B 13 513 509 HOH HOH . 
F 4 HOH B 14 514 510 HOH HOH . 
F 4 HOH B 15 515 511 HOH HOH . 
F 4 HOH B 16 516 512 HOH HOH . 
F 4 HOH B 17 517 514 HOH HOH . 
F 4 HOH B 18 518 515 HOH HOH . 
F 4 HOH B 19 519 516 HOH HOH . 
F 4 HOH B 20 520 517 HOH HOH . 
F 4 HOH B 21 521 518 HOH HOH . 
F 4 HOH B 22 522 519 HOH HOH . 
F 4 HOH B 23 523 520 HOH HOH . 
F 4 HOH B 24 524 521 HOH HOH . 
F 4 HOH B 25 525 522 HOH HOH . 
F 4 HOH B 26 526 523 HOH HOH . 
F 4 HOH B 27 527 524 HOH HOH . 
F 4 HOH B 28 528 525 HOH HOH . 
F 4 HOH B 29 529 526 HOH HOH . 
F 4 HOH B 30 530 527 HOH HOH . 
F 4 HOH B 31 531 528 HOH HOH . 
F 4 HOH B 32 532 530 HOH HOH . 
F 4 HOH B 33 533 531 HOH HOH . 
F 4 HOH B 34 534 532 HOH HOH . 
F 4 HOH B 35 535 534 HOH HOH . 
F 4 HOH B 36 536 535 HOH HOH . 
F 4 HOH B 37 537 536 HOH HOH . 
F 4 HOH B 38 538 537 HOH HOH . 
F 4 HOH B 39 539 538 HOH HOH . 
F 4 HOH B 40 540 539 HOH HOH . 
F 4 HOH B 41 541 540 HOH HOH . 
F 4 HOH B 42 542 541 HOH HOH . 
F 4 HOH B 43 543 542 HOH HOH . 
F 4 HOH B 44 544 543 HOH HOH . 
F 4 HOH B 45 545 545 HOH HOH . 
F 4 HOH B 46 546 546 HOH HOH . 
F 4 HOH B 47 547 547 HOH HOH . 
F 4 HOH B 48 548 549 HOH HOH . 
F 4 HOH B 49 549 550 HOH HOH . 
F 4 HOH B 50 550 551 HOH HOH . 
F 4 HOH B 51 551 552 HOH HOH . 
F 4 HOH B 52 552 554 HOH HOH . 
F 4 HOH B 53 553 556 HOH HOH . 
F 4 HOH B 54 554 557 HOH HOH . 
F 4 HOH B 55 555 558 HOH HOH . 
F 4 HOH B 56 556 559 HOH HOH . 
F 4 HOH B 57 557 560 HOH HOH . 
F 4 HOH B 58 558 561 HOH HOH . 
F 4 HOH B 59 559 562 HOH HOH . 
F 4 HOH B 60 560 563 HOH HOH . 
F 4 HOH B 61 561 564 HOH HOH . 
F 4 HOH B 62 562 565 HOH HOH . 
F 4 HOH B 63 563 566 HOH HOH . 
F 4 HOH B 64 564 567 HOH HOH . 
F 4 HOH B 65 565 568 HOH HOH . 
F 4 HOH B 66 566 569 HOH HOH . 
F 4 HOH B 67 567 570 HOH HOH . 
F 4 HOH B 68 568 571 HOH HOH . 
F 4 HOH B 69 569 572 HOH HOH . 
F 4 HOH B 70 570 573 HOH HOH . 
F 4 HOH B 71 571 574 HOH HOH . 
F 4 HOH B 72 572 575 HOH HOH . 
F 4 HOH B 73 573 576 HOH HOH . 
F 4 HOH B 74 574 578 HOH HOH . 
F 4 HOH B 75 575 579 HOH HOH . 
F 4 HOH B 76 576 581 HOH HOH . 
F 4 HOH B 77 577 582 HOH HOH . 
F 4 HOH B 78 578 583 HOH HOH . 
F 4 HOH B 79 579 584 HOH HOH . 
F 4 HOH B 80 580 585 HOH HOH . 
F 4 HOH B 81 581 586 HOH HOH . 
F 4 HOH B 82 582 587 HOH HOH . 
F 4 HOH B 83 583 588 HOH HOH . 
F 4 HOH B 84 584 589 HOH HOH . 
F 4 HOH B 85 585 590 HOH HOH . 
F 4 HOH B 86 586 591 HOH HOH . 
F 4 HOH B 87 587 593 HOH HOH . 
F 4 HOH B 88 588 594 HOH HOH . 
F 4 HOH B 89 589 595 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 . . . D 3 45.494 11.822 94.695 1 23.59 ? N1 DCS 401 B 1 
HETATM 2 C C2 DCS . . . D 3 44.21 11.946 95.079 1 24.85 ? C2 DCS 401 B 1 
HETATM 3 C C2A DCS . . . D 3 43.271 10.787 94.879 1 24.52 ? C2A DCS 401 B 1 
HETATM 4 C C3 DCS . . . D 3 43.744 13.218 95.696 1 26.3 ? C3 DCS 401 B 1 
HETATM 5 O O3 DCS . . . D 3 42.441 13.347 96.082 1 27.78 ? O3 DCS 401 B 1 
HETATM 6 C C4 DCS . . . D 3 44.75 14.316 95.864 1 26.08 ? C4 DCS 401 B 1 
HETATM 7 C C4A DCS . . . D 3 44.478 15.683 96.47 1 29.61 ? C4A DCS 401 B 1 
HETATM 8 C C5 DCS . . . D 3 46.129 14.031 95.4 1 23.06 ? C5 DCS 401 B 1 
HETATM 9 C C6 DCS . . . D 3 46.418 12.788 94.848 1 24.16 ? C6 DCS 401 B 1 
HETATM 10 C C5A DCS . . . D 3 47.229 15.071 95.52 1 21.56 ? C5A DCS 401 B 1 
HETATM 11 O O4P DCS . . . D 3 47.456 15.409 96.896 1 19.44 ? O4P DCS 401 B 1 
HETATM 12 P P DCS . . . D 3 48.575 16.516 97.265 1 19.09 ? P DCS 401 B 1 
HETATM 13 O O1P DCS . . . D 3 49.835 15.983 96.61 1 17.31 ? O1P DCS 401 B 1 
HETATM 14 O O2P DCS . . . D 3 48.038 17.755 96.592 1 20.59 ? O2P DCS 401 B 1 
HETATM 15 O O3P DCS . . . D 3 48.604 16.551 98.79 1 19.73 ? O3P DCS 401 B 1 
HETATM 16 N N DCS . . . D 3 43.176 15.862 97.073 1 35.48 ? N DCS 401 B 1 
HETATM 17 C CA DCS . . . D 3 42.825 17.145 97.67 1 41.79 ? CA DCS 401 B 1 
HETATM 18 C C DCS . . . D 3 41.624 17.021 98.525 1 38.7 ? C DCS 401 B 1 
HETATM 19 O O DCS . . . D 3 40.687 16.322 98.202 1 42.61 ? O DCS 401 B 1 
HETATM 20 N ND DCS . . . D 3 41.784 17.74 99.63 1 43.38 ? ND DCS 401 B 1 
HETATM 21 O OG DCS . . . D 3 43 18.279 99.702 1 57.59 ? OG DCS 401 B 1 
HETATM 22 C CB DCS . . . D 3 43.829 17.765 98.645 1 49.38 ? CB DCS 401 B 1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    31 
_model_server_stats.query_time_ms           801 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           22 
#