data_4GTF
#
_model_server_result.job_id            33TPS6dbc3p7-8tHIE5fEA 
_model_server_result.datetime_utc      '2024-11-15 15:59:36' 
_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          4gtf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    4GTF 
#
_exptl.entry_id    4GTF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_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         90 
_cell.entry_id            4GTF 
_cell.length_a            109.81 
_cell.length_b            109.81 
_cell.length_c            122.29 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4GTF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        98 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 41 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_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,F 
_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' 7_455 y-1/2,x+1/2,-z+1/2 0 1 0 1 0 0 0 0 -1 -54.905 54.905 61.145 
3 'crystal symmetry operation' 10_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -109.81 0 0 
4 'crystal symmetry operation' 16_445 -y-1/2,-x-1/2,-z+1/2 0 -1 0 -1 0 0 0 0 -1 -54.905 -54.905 61.145 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C9 H13 N2 O8 P' 
_chem_comp.formula_weight    308.182 
_chem_comp.id                UMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     DUMP 
#
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 UMP sing 508 n n 
N1 C6 UMP sing 509 n n 
N1 C1' UMP sing 510 n n 
C2 N3 UMP sing 511 n n 
C2 O2 UMP doub 512 n n 
N3 C4 UMP sing 513 n n 
N3 HN3 UMP sing 514 n n 
C4 C5 UMP sing 515 n n 
C4 O4 UMP doub 516 n n 
C5 C6 UMP doub 517 n n 
C5 H5 UMP sing 518 n n 
C6 H6 UMP sing 519 n n 
C1' C2' UMP sing 520 n n 
C1' O4' UMP sing 521 n n 
C1' H1' UMP sing 522 n n 
C2' C3' UMP sing 523 n n 
C2' H2' UMP sing 524 n n 
C2' "H2''" UMP sing 525 n n 
C3' C4' UMP sing 526 n n 
C3' O3' UMP sing 527 n n 
C3' H3' UMP sing 528 n n 
C4' O4' UMP sing 529 n n 
C4' C5' UMP sing 530 n n 
C4' H4' UMP sing 531 n n 
O3' HO3' UMP sing 532 n n 
C5' O5' UMP sing 533 n n 
C5' H5' UMP sing 534 n n 
C5' "H5''" UMP sing 535 n n 
O5' P UMP sing 536 n n 
P OP1 UMP doub 537 n n 
P OP2 UMP sing 538 n n 
P OP3 UMP sing 539 n n 
OP2 HOP2 UMP sing 540 n n 
OP3 HOP3 UMP sing 541 n n 
#
_atom_sites.entry_id                     4GTF 
_atom_sites.fract_transf_matrix[1][1]    0.009107 
_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]    0.009107 
_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]    0.008177 
_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 FAD A 1 301 300 FAD FAD . 
C 3 UMP A 1 302 303 UMP UMP . 
D 4 MEF A 1 303 308 MEF MEF . 
E 5 CL A 1 304 310 CL CL . 
F 6 HOH A 1 401 1 HOH HOH . 
F 6 HOH A 2 402 2 HOH HOH . 
F 6 HOH A 3 403 3 HOH HOH . 
F 6 HOH A 4 404 4 HOH HOH . 
F 6 HOH A 5 405 5 HOH HOH . 
F 6 HOH A 6 406 6 HOH HOH . 
F 6 HOH A 7 407 7 HOH HOH . 
F 6 HOH A 8 408 8 HOH HOH . 
F 6 HOH A 9 409 9 HOH HOH . 
F 6 HOH A 10 410 10 HOH HOH . 
F 6 HOH A 11 411 11 HOH HOH . 
F 6 HOH A 12 412 12 HOH HOH . 
F 6 HOH A 13 413 13 HOH HOH . 
F 6 HOH A 14 414 14 HOH HOH . 
F 6 HOH A 15 415 15 HOH HOH . 
F 6 HOH A 16 416 16 HOH HOH . 
F 6 HOH A 17 417 17 HOH HOH . 
F 6 HOH A 18 418 18 HOH HOH . 
F 6 HOH A 19 419 19 HOH HOH . 
F 6 HOH A 20 420 20 HOH HOH . 
F 6 HOH A 21 421 21 HOH HOH . 
F 6 HOH A 22 422 22 HOH HOH . 
F 6 HOH A 23 423 23 HOH HOH . 
F 6 HOH A 24 424 24 HOH HOH . 
F 6 HOH A 25 425 25 HOH HOH . 
F 6 HOH A 26 426 26 HOH HOH . 
F 6 HOH A 27 427 27 HOH HOH . 
F 6 HOH A 28 428 28 HOH HOH . 
F 6 HOH A 29 429 29 HOH HOH . 
F 6 HOH A 30 430 30 HOH HOH . 
F 6 HOH A 31 431 31 HOH HOH . 
F 6 HOH A 32 432 32 HOH HOH . 
F 6 HOH A 33 433 33 HOH HOH . 
F 6 HOH A 34 434 34 HOH HOH . 
F 6 HOH A 35 435 35 HOH HOH . 
F 6 HOH A 36 436 36 HOH HOH . 
F 6 HOH A 37 437 37 HOH HOH . 
F 6 HOH A 38 438 38 HOH HOH . 
F 6 HOH A 39 439 39 HOH HOH . 
F 6 HOH A 40 440 40 HOH HOH . 
F 6 HOH A 41 441 41 HOH HOH . 
F 6 HOH A 42 442 42 HOH HOH . 
F 6 HOH A 43 443 43 HOH HOH . 
F 6 HOH A 44 444 44 HOH HOH . 
F 6 HOH A 45 445 45 HOH HOH . 
F 6 HOH A 46 446 46 HOH HOH . 
F 6 HOH A 47 447 47 HOH HOH . 
F 6 HOH A 48 448 48 HOH HOH . 
F 6 HOH A 49 449 49 HOH HOH . 
F 6 HOH A 50 450 50 HOH HOH . 
F 6 HOH A 51 451 51 HOH HOH . 
F 6 HOH A 52 452 52 HOH HOH . 
F 6 HOH A 53 453 53 HOH HOH . 
F 6 HOH A 54 454 54 HOH HOH . 
F 6 HOH A 55 455 55 HOH HOH . 
F 6 HOH A 56 456 56 HOH HOH . 
F 6 HOH A 57 457 57 HOH HOH . 
F 6 HOH A 58 458 58 HOH HOH . 
F 6 HOH A 59 459 59 HOH HOH . 
F 6 HOH A 60 460 60 HOH HOH . 
F 6 HOH A 61 461 61 HOH HOH . 
F 6 HOH A 62 462 62 HOH HOH . 
F 6 HOH A 63 463 63 HOH HOH . 
F 6 HOH A 64 464 64 HOH HOH . 
F 6 HOH A 65 465 65 HOH HOH . 
F 6 HOH A 66 466 66 HOH HOH . 
F 6 HOH A 67 467 67 HOH HOH . 
F 6 HOH A 68 468 68 HOH HOH . 
F 6 HOH A 69 469 69 HOH HOH . 
F 6 HOH A 70 470 70 HOH HOH . 
F 6 HOH A 71 471 71 HOH HOH . 
F 6 HOH A 72 472 72 HOH HOH . 
F 6 HOH A 73 473 73 HOH HOH . 
F 6 HOH A 74 474 74 HOH HOH . 
F 6 HOH A 75 475 75 HOH HOH . 
F 6 HOH A 76 476 76 HOH HOH . 
F 6 HOH A 77 477 77 HOH HOH . 
F 6 HOH A 78 478 78 HOH HOH . 
F 6 HOH A 79 479 79 HOH HOH . 
F 6 HOH A 80 480 80 HOH HOH . 
F 6 HOH A 81 481 81 HOH HOH . 
F 6 HOH A 82 482 82 HOH HOH . 
F 6 HOH A 83 483 83 HOH HOH . 
F 6 HOH A 84 484 84 HOH HOH . 
F 6 HOH A 85 485 85 HOH HOH . 
F 6 HOH A 86 486 86 HOH HOH . 
F 6 HOH A 87 487 87 HOH HOH . 
F 6 HOH A 88 488 88 HOH HOH . 
F 6 HOH A 89 489 89 HOH HOH . 
F 6 HOH A 90 490 90 HOH HOH . 
F 6 HOH A 91 491 91 HOH HOH . 
F 6 HOH A 92 492 92 HOH HOH . 
F 6 HOH A 93 493 93 HOH HOH . 
F 6 HOH A 94 494 94 HOH HOH . 
F 6 HOH A 95 495 95 HOH HOH . 
F 6 HOH A 96 496 96 HOH HOH . 
F 6 HOH A 97 497 97 HOH HOH . 
F 6 HOH A 98 498 98 HOH HOH . 
F 6 HOH A 99 499 99 HOH HOH . 
F 6 HOH A 100 500 100 HOH HOH . 
F 6 HOH A 101 501 101 HOH HOH . 
F 6 HOH A 102 502 102 HOH HOH . 
F 6 HOH A 103 503 103 HOH HOH . 
F 6 HOH A 104 504 104 HOH HOH . 
F 6 HOH A 105 505 105 HOH HOH . 
F 6 HOH A 106 506 106 HOH HOH . 
F 6 HOH A 107 507 107 HOH HOH . 
F 6 HOH A 108 508 108 HOH HOH . 
F 6 HOH A 109 509 109 HOH HOH . 
F 6 HOH A 110 510 110 HOH HOH . 
F 6 HOH A 111 511 111 HOH HOH . 
F 6 HOH A 112 512 112 HOH HOH . 
F 6 HOH A 113 513 113 HOH HOH . 
F 6 HOH A 114 514 114 HOH HOH . 
F 6 HOH A 115 515 115 HOH HOH . 
F 6 HOH A 116 516 116 HOH HOH . 
F 6 HOH A 117 517 117 HOH HOH . 
F 6 HOH A 118 518 118 HOH HOH . 
F 6 HOH A 119 519 119 HOH HOH . 
F 6 HOH A 120 520 120 HOH HOH . 
F 6 HOH A 121 521 121 HOH HOH . 
F 6 HOH A 122 522 122 HOH HOH . 
F 6 HOH A 123 523 123 HOH HOH . 
F 6 HOH A 124 524 124 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 UMP . . . C 3 -49.184 -17.985 28.008 1 25.54 ? N1 UMP 302 A 1 
HETATM 2 C C2 UMP . . . C 3 -49.915 -17.798 29.166 1 24.67 ? C2 UMP 302 A 1 
HETATM 3 N N3 UMP . . . C 3 -50.544 -18.874 29.661 1 25.58 ? N3 UMP 302 A 1 
HETATM 4 C C4 UMP . . . C 3 -50.555 -20.1 29.089 1 27.13 ? C4 UMP 302 A 1 
HETATM 5 C C5 UMP . . . C 3 -49.852 -20.297 27.897 1 26.05 ? C5 UMP 302 A 1 
HETATM 6 C C6 UMP . . . C 3 -49.194 -19.182 27.382 1 25.62 ? C6 UMP 302 A 1 
HETATM 7 O O2 UMP . . . C 3 -49.936 -16.674 29.711 1 25.22 ? O2 UMP 302 A 1 
HETATM 8 O O4 UMP . . . C 3 -51.18 -21.033 29.634 1 26.24 ? O4 UMP 302 A 1 
HETATM 9 C C1' UMP . . . C 3 -48.449 -16.828 27.477 1 26.31 ? C1' UMP 302 A 1 
HETATM 10 C C2' UMP . . . C 3 -47.184 -16.572 28.283 1 25.23 ? C2' UMP 302 A 1 
HETATM 11 C C3' UMP . . . C 3 -46.074 -16.342 27.274 1 25.02 ? C3' UMP 302 A 1 
HETATM 12 C C4' UMP . . . C 3 -46.548 -17.098 26.046 1 25.45 ? C4' UMP 302 A 1 
HETATM 13 O O3' UMP . . . C 3 -45.985 -14.934 26.971 1 25.87 ? O3' UMP 302 A 1 
HETATM 14 O O4' UMP . . . C 3 -47.98 -17.12 26.162 1 24.46 ? O4' UMP 302 A 1 
HETATM 15 C C5' UMP . . . C 3 -45.96 -18.511 25.896 1 26.76 ? C5' UMP 302 A 1 
HETATM 16 O O5' UMP . . . C 3 -46.143 -19.165 27.146 1 26.47 ? O5' UMP 302 A 1 
HETATM 17 P P UMP . . . C 3 -45.899 -20.737 27.336 1 26.69 ? P UMP 302 A 1 
HETATM 18 O OP1 UMP . . . C 3 -45.951 -21.027 28.828 1 25.75 ? OP1 UMP 302 A 1 
HETATM 19 O OP2 UMP . . . C 3 -46.944 -21.47 26.516 1 28.78 ? OP2 UMP 302 A 1 
HETATM 20 O OP3 UMP . . . C 3 -44.542 -21.018 26.722 1 26.58 ? OP3 UMP 302 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#