data_4D9F
#
_model_server_result.job_id            BFY8CLePVvEE4axYreuqjw 
_model_server_result.datetime_utc      '2024-12-02 23:25:32' 
_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          4d9f 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":402}' 
#
_entry.id    4D9F 
#
_exptl.entry_id    4D9F 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          121.28 
_cell.angle_gamma         90 
_cell.entry_id            4D9F 
_cell.length_a            66.16 
_cell.length_b            167.51 
_cell.length_c            68.773 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4D9F 
_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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,L,M 1 1 
C,D,I,J,K,N,O 2 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 F N N 
? 3 H N N 
? 3 I N N 
? 3 K N N 
#
_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 100 n y 
N1 C6 DCS sing 101 n y 
C2 C2A DCS sing 102 n n 
C2 C3 DCS sing 103 n y 
C2A H2A1 DCS sing 104 n n 
C2A H2A2 DCS sing 105 n n 
C2A H2A3 DCS sing 106 n n 
C3 O3 DCS sing 107 n n 
C3 C4 DCS doub 108 n y 
O3 HO3 DCS sing 109 n n 
C4 C4A DCS sing 110 n n 
C4 C5 DCS sing 111 n y 
C4A N DCS sing 112 n n 
C4A H4A1 DCS sing 113 n n 
C4A H4A2 DCS sing 114 n n 
C5 C6 DCS doub 115 n y 
C5 C5A DCS sing 116 n n 
C6 H6 DCS sing 117 n n 
C5A O4P DCS sing 118 n n 
C5A H5A1 DCS sing 119 n n 
C5A H5A2 DCS sing 120 n n 
O4P P DCS sing 121 n n 
P O1P DCS doub 122 n n 
P O2P DCS sing 123 n n 
P O3P DCS sing 124 n n 
O2P HOP2 DCS sing 125 n n 
O3P HOP3 DCS sing 126 n n 
N CA DCS sing 127 n n 
N HN DCS sing 128 n n 
CA C DCS sing 129 n n 
CA CB DCS sing 130 n n 
CA HA DCS sing 131 n n 
C O DCS doub 132 n n 
C ND DCS sing 133 n n 
ND OG DCS sing 134 n n 
ND HND DCS sing 135 n n 
OG CB DCS sing 136 n n 
CB HB1 DCS sing 137 n n 
CB HB2 DCS sing 138 n n 
#
_atom_sites.entry_id                     4D9F 
_atom_sites.fract_transf_matrix[1][1]    0.015115 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.009183 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00597 
_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]    0.017014 
_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 BEN A 1 401 401 BEN BEN . 
F 3 DCS A 1 402 402 DCS DCS . 
G 2 BEN B 1 401 401 BEN BEN . 
H 3 DCS B 1 402 402 DCS DCS . 
I 3 DCS C 1 401 401 DCS DCS . 
J 2 BEN D 1 401 401 BEN BEN . 
K 3 DCS D 1 402 402 DCS DCS . 
L 4 HOH A 1 501 501 HOH HOH . 
L 4 HOH A 2 502 502 HOH HOH . 
L 4 HOH A 3 503 503 HOH HOH . 
L 4 HOH A 4 504 504 HOH HOH . 
L 4 HOH A 5 505 505 HOH HOH . 
L 4 HOH A 6 506 506 HOH HOH . 
L 4 HOH A 7 507 507 HOH HOH . 
L 4 HOH A 8 508 508 HOH HOH . 
L 4 HOH A 9 509 510 HOH HOH . 
L 4 HOH A 10 510 511 HOH HOH . 
L 4 HOH A 11 511 512 HOH HOH . 
L 4 HOH A 12 512 513 HOH HOH . 
L 4 HOH A 13 513 514 HOH HOH . 
L 4 HOH A 14 514 515 HOH HOH . 
L 4 HOH A 15 515 516 HOH HOH . 
L 4 HOH A 16 516 517 HOH HOH . 
L 4 HOH A 17 517 518 HOH HOH . 
L 4 HOH A 18 518 519 HOH HOH . 
L 4 HOH A 19 519 520 HOH HOH . 
L 4 HOH A 20 520 521 HOH HOH . 
L 4 HOH A 21 521 522 HOH HOH . 
L 4 HOH A 22 522 523 HOH HOH . 
L 4 HOH A 23 523 524 HOH HOH . 
L 4 HOH A 24 524 525 HOH HOH . 
L 4 HOH A 25 525 526 HOH HOH . 
L 4 HOH A 26 526 527 HOH HOH . 
L 4 HOH A 27 527 528 HOH HOH . 
L 4 HOH A 28 528 529 HOH HOH . 
L 4 HOH A 29 529 530 HOH HOH . 
L 4 HOH A 30 530 531 HOH HOH . 
L 4 HOH A 31 531 532 HOH HOH . 
L 4 HOH A 32 532 533 HOH HOH . 
L 4 HOH A 33 533 534 HOH HOH . 
L 4 HOH A 34 534 535 HOH HOH . 
L 4 HOH A 35 535 536 HOH HOH . 
L 4 HOH A 36 536 537 HOH HOH . 
L 4 HOH A 37 537 538 HOH HOH . 
L 4 HOH A 38 538 539 HOH HOH . 
L 4 HOH A 39 539 540 HOH HOH . 
L 4 HOH A 40 540 541 HOH HOH . 
L 4 HOH A 41 541 542 HOH HOH . 
L 4 HOH A 42 542 543 HOH HOH . 
L 4 HOH A 43 543 544 HOH HOH . 
L 4 HOH A 44 544 545 HOH HOH . 
L 4 HOH A 45 545 546 HOH HOH . 
L 4 HOH A 46 546 548 HOH HOH . 
L 4 HOH A 47 547 549 HOH HOH . 
L 4 HOH A 48 548 550 HOH HOH . 
L 4 HOH A 49 549 551 HOH HOH . 
L 4 HOH A 50 550 552 HOH HOH . 
L 4 HOH A 51 551 553 HOH HOH . 
L 4 HOH A 52 552 554 HOH HOH . 
L 4 HOH A 53 553 503 HOH HOH . 
M 4 HOH B 1 501 509 HOH HOH . 
M 4 HOH B 2 502 501 HOH HOH . 
M 4 HOH B 3 503 502 HOH HOH . 
M 4 HOH B 4 504 504 HOH HOH . 
M 4 HOH B 5 505 505 HOH HOH . 
M 4 HOH B 6 506 506 HOH HOH . 
M 4 HOH B 7 507 507 HOH HOH . 
M 4 HOH B 8 508 508 HOH HOH . 
M 4 HOH B 9 509 509 HOH HOH . 
M 4 HOH B 10 510 510 HOH HOH . 
M 4 HOH B 11 511 511 HOH HOH . 
M 4 HOH B 12 512 512 HOH HOH . 
M 4 HOH B 13 513 513 HOH HOH . 
M 4 HOH B 14 514 514 HOH HOH . 
M 4 HOH B 15 515 515 HOH HOH . 
M 4 HOH B 16 516 516 HOH HOH . 
M 4 HOH B 17 517 517 HOH HOH . 
M 4 HOH B 18 518 518 HOH HOH . 
M 4 HOH B 19 519 519 HOH HOH . 
M 4 HOH B 20 520 520 HOH HOH . 
M 4 HOH B 21 521 521 HOH HOH . 
M 4 HOH B 22 522 522 HOH HOH . 
M 4 HOH B 23 523 523 HOH HOH . 
M 4 HOH B 24 524 524 HOH HOH . 
M 4 HOH B 25 525 525 HOH HOH . 
M 4 HOH B 26 526 526 HOH HOH . 
M 4 HOH B 27 527 527 HOH HOH . 
M 4 HOH B 28 528 528 HOH HOH . 
M 4 HOH B 29 529 529 HOH HOH . 
M 4 HOH B 30 530 530 HOH HOH . 
M 4 HOH B 31 531 531 HOH HOH . 
M 4 HOH B 32 532 532 HOH HOH . 
M 4 HOH B 33 533 533 HOH HOH . 
M 4 HOH B 34 534 534 HOH HOH . 
M 4 HOH B 35 535 535 HOH HOH . 
M 4 HOH B 36 536 536 HOH HOH . 
M 4 HOH B 37 537 537 HOH HOH . 
M 4 HOH B 38 538 538 HOH HOH . 
M 4 HOH B 39 539 539 HOH HOH . 
N 4 HOH C 1 501 547 HOH HOH . 
N 4 HOH C 2 502 501 HOH HOH . 
N 4 HOH C 3 503 502 HOH HOH . 
N 4 HOH C 4 504 503 HOH HOH . 
N 4 HOH C 5 505 504 HOH HOH . 
N 4 HOH C 6 506 505 HOH HOH . 
N 4 HOH C 7 507 506 HOH HOH . 
N 4 HOH C 8 508 507 HOH HOH . 
N 4 HOH C 9 509 508 HOH HOH . 
N 4 HOH C 10 510 509 HOH HOH . 
N 4 HOH C 11 511 510 HOH HOH . 
N 4 HOH C 12 512 511 HOH HOH . 
N 4 HOH C 13 513 512 HOH HOH . 
N 4 HOH C 14 514 513 HOH HOH . 
N 4 HOH C 15 515 514 HOH HOH . 
N 4 HOH C 16 516 515 HOH HOH . 
N 4 HOH C 17 517 516 HOH HOH . 
N 4 HOH C 18 518 517 HOH HOH . 
N 4 HOH C 19 519 518 HOH HOH . 
N 4 HOH C 20 520 520 HOH HOH . 
N 4 HOH C 21 521 521 HOH HOH . 
N 4 HOH C 22 522 522 HOH HOH . 
N 4 HOH C 23 523 524 HOH HOH . 
N 4 HOH C 24 524 525 HOH HOH . 
N 4 HOH C 25 525 526 HOH HOH . 
N 4 HOH C 26 526 527 HOH HOH . 
N 4 HOH C 27 527 528 HOH HOH . 
N 4 HOH C 28 528 529 HOH HOH . 
N 4 HOH C 29 529 530 HOH HOH . 
O 4 HOH D 1 501 519 HOH HOH . 
O 4 HOH D 2 502 523 HOH HOH . 
O 4 HOH D 3 503 501 HOH HOH . 
O 4 HOH D 4 504 502 HOH HOH . 
O 4 HOH D 5 505 503 HOH HOH . 
O 4 HOH D 6 506 504 HOH HOH . 
O 4 HOH D 7 507 505 HOH HOH . 
O 4 HOH D 8 508 506 HOH HOH . 
O 4 HOH D 9 509 507 HOH HOH . 
O 4 HOH D 10 510 508 HOH HOH . 
O 4 HOH D 11 511 509 HOH HOH . 
O 4 HOH D 12 512 510 HOH HOH . 
O 4 HOH D 13 513 511 HOH HOH . 
O 4 HOH D 14 514 512 HOH HOH . 
O 4 HOH D 15 515 513 HOH HOH . 
O 4 HOH D 16 516 514 HOH HOH . 
O 4 HOH D 17 517 515 HOH HOH . 
O 4 HOH D 18 518 516 HOH HOH . 
O 4 HOH D 19 519 517 HOH HOH . 
O 4 HOH D 20 520 518 HOH HOH . 
O 4 HOH D 21 521 519 HOH HOH . 
O 4 HOH D 22 522 520 HOH HOH . 
O 4 HOH D 23 523 521 HOH HOH . 
O 4 HOH D 24 524 522 HOH HOH . 
O 4 HOH D 25 525 523 HOH HOH . 
O 4 HOH D 26 526 524 HOH HOH . 
O 4 HOH D 27 527 525 HOH HOH . 
O 4 HOH D 28 528 526 HOH HOH . 
O 4 HOH D 29 529 527 HOH HOH . 
O 4 HOH D 30 530 528 HOH HOH . 
O 4 HOH D 31 531 529 HOH HOH . 
O 4 HOH D 32 532 530 HOH HOH . 
O 4 HOH D 33 533 531 HOH HOH . 
O 4 HOH D 34 534 532 HOH HOH . 
O 4 HOH D 35 535 533 HOH HOH . 
O 4 HOH D 36 536 534 HOH HOH . 
O 4 HOH D 37 537 535 HOH HOH . 
O 4 HOH D 38 538 536 HOH HOH . 
O 4 HOH D 39 539 537 HOH HOH . 
O 4 HOH D 40 540 538 HOH HOH . 
O 4 HOH D 41 541 539 HOH HOH . 
O 4 HOH D 42 542 540 HOH HOH . 
O 4 HOH D 43 543 541 HOH HOH . 
O 4 HOH D 44 544 542 HOH HOH . 
O 4 HOH D 45 545 543 HOH HOH . 
O 4 HOH D 46 546 544 HOH HOH . 
O 4 HOH D 47 547 545 HOH HOH . 
O 4 HOH D 48 548 546 HOH HOH . 
O 4 HOH D 49 549 547 HOH HOH . 
O 4 HOH D 50 550 548 HOH HOH . 
O 4 HOH D 51 551 549 HOH HOH . 
O 4 HOH D 52 552 550 HOH HOH . 
O 4 HOH D 53 553 551 HOH HOH . 
O 4 HOH D 54 554 552 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 . . . K 3 -2.886 86.822 18.267 1 23.86 ? N1 DCS 402 D 1 
HETATM 2 C C2 DCS . . . K 3 -2.441 85.562 18.485 1 24.05 ? C2 DCS 402 D 1 
HETATM 3 C C2A DCS . . . K 3 -1.262 85.044 17.703 1 23.56 ? C2A DCS 402 D 1 
HETATM 4 C C3 DCS . . . K 3 -3.121 84.696 19.485 1 24.14 ? C3 DCS 402 D 1 
HETATM 5 O O3 DCS . . . K 3 -2.683 83.427 19.708 1 24.5 ? O3 DCS 402 D 1 
HETATM 6 C C4 DCS . . . K 3 -4.286 85.247 20.225 1 24.29 ? C4 DCS 402 D 1 
HETATM 7 C C4A DCS . . . K 3 -4.979 84.357 21.252 1 24.98 ? C4A DCS 402 D 1 
HETATM 8 C C5 DCS . . . K 3 -4.662 86.657 19.885 1 23.79 ? C5 DCS 402 D 1 
HETATM 9 C C6 DCS . . . K 3 -3.931 87.352 18.923 1 23.79 ? C6 DCS 402 D 1 
HETATM 10 C C5A DCS . . . K 3 -5.813 87.392 20.524 1 23.5 ? C5A DCS 402 D 1 
HETATM 11 O O4P DCS . . . K 3 -5.336 88.178 21.613 1 23.13 ? O4P DCS 402 D 1 
HETATM 12 P P DCS . . . K 3 -6.184 88.212 22.974 1 22.71 ? P DCS 402 D 1 
HETATM 13 O O1P DCS . . . K 3 -6.474 86.758 23.261 1 22.48 ? O1P DCS 402 D 1 
HETATM 14 O O2P DCS . . . K 3 -5.258 88.862 23.967 1 22.88 ? O2P DCS 402 D 1 
HETATM 15 O O3P DCS . . . K 3 -7.392 89.041 22.612 1 22.48 ? O3P DCS 402 D 1 
HETATM 16 N N DCS . . . K 3 -6.396 84.62 21.471 1 25.97 ? N DCS 402 D 1 
HETATM 17 C CA DCS . . . K 3 -7.382 83.582 21.212 0.7 26.2 ? CA DCS 402 D 1 
HETATM 18 C C DCS . . . K 3 -7.593 82.593 22.319 0.7 26.34 ? C DCS 402 D 1 
HETATM 19 O O DCS . . . K 3 -6.693 81.988 22.877 0.7 26.51 ? O DCS 402 D 1 
HETATM 20 N ND DCS . . . K 3 -8.891 82.473 22.573 0.7 26.59 ? ND DCS 402 D 1 
HETATM 21 O OG DCS . . . K 3 -9.591 83.426 21.93 0.7 26.79 ? OG DCS 402 D 1 
HETATM 22 C CB DCS . . . K 3 -8.782 84.15 20.989 0.7 26.36 ? CB DCS 402 D 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           266 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           22 
#