data_4DKB # _model_server_result.job_id ZzXutsdi_quuUPvTT-pV5g _model_server_result.datetime_utc '2024-12-01 21:19:11' _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 4dkb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 4DKB # _exptl.entry_id 4DKB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 387.177 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE" _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 4DKB _cell.length_a 68.47 _cell.length_b 68.47 _cell.length_c 123.87 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DKB _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 61.935 # _struct_asym.details ? _struct_asym.entity_id 3 _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 OE2 GLU 51 A GLU 48 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc2 A OE1 GLU 51 A GLU 48 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc3 A OE2 GLU 54 A GLU 51 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc4 A OE1 GLU 54 A GLU 51 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? metalc ? metalc5 A OE1 GLU 54 A GLU 51 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc6 A OE1 GLU 79 A GLU 76 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc7 A OD2 ASP 82 A ASP 79 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc8 B CA CA . A CA 301 1_555 D O2A DUN . A DUN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc9 B CA CA . A CA 301 1_555 D O3B DUN . A DUN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc10 B CA CA . A CA 301 1_555 E O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc11 B CA CA . A CA 301 1_555 E O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc12 C CA CA . A CA 302 1_555 D O3B DUN . A DUN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc13 C CA CA . A CA 302 1_555 E O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? # _chem_comp.formula 'C9 H15 N3 O10 P2' _chem_comp.formula_weight 387.177 _chem_comp.id DUN _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 2,4(1H,3H)-PYRIMIDINEDIONE;1-[2-DEOXY-5-O-[HYDROXY(PHOSPHONOAMINO)PHOSPHINYL]-BETA-D-ERYTHRO-PENTOFURANOSYL]- # 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 DUN sing 83 n y N1 C6 DUN sing 84 n y N1 C1' DUN sing 85 n n C2 N3 DUN sing 86 n y C2 O2 DUN doub 87 n n N3 C4 DUN sing 88 n y N3 H3 DUN sing 89 n n C4 C5 DUN sing 90 n y C4 O4 DUN doub 91 n n C5 C6 DUN doub 92 n y C5 H5 DUN sing 93 n n C6 H6 DUN sing 94 n n C1' C2' DUN sing 95 n n C1' O4' DUN sing 96 n n C1' H1' DUN sing 97 n n C2' C3' DUN sing 98 n n C2' "H2'1" DUN sing 99 n n C2' "H2'2" DUN sing 100 n n C3' C4' DUN sing 101 n n C3' O3' DUN sing 102 n n C3' H3' DUN sing 103 n n C4' O4' DUN sing 104 n n C4' C5' DUN sing 105 n n C4' H4' DUN sing 106 n n O3' HA DUN sing 107 n n C5' O5' DUN sing 108 n n C5' "H5'1" DUN sing 109 n n C5' "H5'2" DUN sing 110 n n O5' PA DUN sing 111 n n PA O1A DUN sing 112 n n PA O2A DUN doub 113 n n PA N3A DUN sing 114 n n O1A H1A DUN sing 115 n n PB O1B DUN sing 116 n n PB O2B DUN doub 117 n n PB O3B DUN sing 118 n n PB N3A DUN sing 119 n n O1B H1B DUN sing 120 n n O3B H3B DUN sing 121 n n N3A H3A DUN sing 122 n n # _atom_sites.entry_id 4DKB _atom_sites.fract_transf_matrix[1][1] 0.014605 _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] 0.014605 _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] 0.008073 _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 CA A 1 301 1 CA CA . C 2 CA A 1 302 2 CA CA . D 3 DUN A 1 303 1 DUN DUN . E 4 HOH A 1 401 1 HOH HOH . E 4 HOH A 2 402 2 HOH HOH . E 4 HOH A 3 403 3 HOH HOH . E 4 HOH A 4 404 4 HOH HOH . E 4 HOH A 5 405 5 HOH HOH . E 4 HOH A 6 406 6 HOH HOH . E 4 HOH A 7 407 7 HOH HOH . E 4 HOH A 8 408 8 HOH HOH . E 4 HOH A 9 409 9 HOH HOH . E 4 HOH A 10 410 10 HOH HOH . E 4 HOH A 11 411 11 HOH HOH . E 4 HOH A 12 412 12 HOH HOH . E 4 HOH A 13 413 13 HOH HOH . E 4 HOH A 14 414 14 HOH HOH . E 4 HOH A 15 415 15 HOH HOH . E 4 HOH A 16 416 16 HOH HOH . E 4 HOH A 17 417 17 HOH HOH . E 4 HOH A 18 418 18 HOH HOH . E 4 HOH A 19 419 19 HOH HOH . E 4 HOH A 20 420 20 HOH HOH . E 4 HOH A 21 421 21 HOH HOH . E 4 HOH A 22 422 22 HOH HOH . E 4 HOH A 23 423 23 HOH HOH . E 4 HOH A 24 424 24 HOH HOH . E 4 HOH A 25 425 25 HOH HOH . E 4 HOH A 26 426 26 HOH HOH . E 4 HOH A 27 427 27 HOH HOH . E 4 HOH A 28 428 28 HOH HOH . E 4 HOH A 29 429 29 HOH HOH . E 4 HOH A 30 430 30 HOH HOH . E 4 HOH A 31 431 31 HOH HOH . E 4 HOH A 32 432 32 HOH HOH . E 4 HOH A 33 433 33 HOH HOH . E 4 HOH A 34 434 34 HOH HOH . E 4 HOH A 35 435 35 HOH HOH . E 4 HOH A 36 436 36 HOH HOH . E 4 HOH A 37 437 37 HOH HOH . E 4 HOH A 38 438 38 HOH HOH . E 4 HOH A 39 439 39 HOH HOH . E 4 HOH A 40 440 40 HOH HOH . E 4 HOH A 41 441 42 HOH HOH . E 4 HOH A 42 442 43 HOH HOH . E 4 HOH A 43 443 45 HOH HOH . E 4 HOH A 44 444 46 HOH HOH . E 4 HOH A 45 445 47 HOH HOH . E 4 HOH A 46 446 48 HOH HOH . E 4 HOH A 47 447 49 HOH HOH . E 4 HOH A 48 448 50 HOH HOH . E 4 HOH A 49 449 51 HOH HOH . E 4 HOH A 50 450 52 HOH HOH . E 4 HOH A 51 451 53 HOH HOH . E 4 HOH A 52 452 54 HOH HOH . E 4 HOH A 53 453 55 HOH HOH . E 4 HOH A 54 454 56 HOH HOH . E 4 HOH A 55 455 57 HOH HOH . E 4 HOH A 56 456 58 HOH HOH . E 4 HOH A 57 457 59 HOH HOH . E 4 HOH A 58 458 60 HOH HOH . E 4 HOH A 59 459 62 HOH HOH . E 4 HOH A 60 460 63 HOH HOH . E 4 HOH A 61 461 64 HOH HOH . E 4 HOH A 62 462 65 HOH HOH . E 4 HOH A 63 463 66 HOH HOH . E 4 HOH A 64 464 67 HOH HOH . E 4 HOH A 65 465 68 HOH HOH . E 4 HOH A 66 466 69 HOH HOH . E 4 HOH A 67 467 70 HOH HOH . E 4 HOH A 68 468 71 HOH HOH . E 4 HOH A 69 469 72 HOH HOH . E 4 HOH A 70 470 73 HOH HOH . E 4 HOH A 71 471 74 HOH HOH . E 4 HOH A 72 472 75 HOH HOH . E 4 HOH A 73 473 77 HOH HOH . E 4 HOH A 74 474 78 HOH HOH . E 4 HOH A 75 475 79 HOH HOH . E 4 HOH A 76 476 81 HOH HOH . E 4 HOH A 77 477 82 HOH HOH . E 4 HOH A 78 478 83 HOH HOH . E 4 HOH A 79 479 84 HOH HOH . E 4 HOH A 80 480 85 HOH HOH . E 4 HOH A 81 481 86 HOH HOH . E 4 HOH A 82 482 87 HOH HOH . E 4 HOH A 83 483 88 HOH HOH . E 4 HOH A 84 484 89 HOH HOH . E 4 HOH A 85 485 90 HOH HOH . E 4 HOH A 86 486 91 HOH HOH . E 4 HOH A 87 487 92 HOH HOH . E 4 HOH A 88 488 93 HOH HOH . E 4 HOH A 89 489 94 HOH HOH . E 4 HOH A 90 490 95 HOH HOH . E 4 HOH A 91 491 96 HOH HOH . E 4 HOH A 92 492 97 HOH HOH . E 4 HOH A 93 493 98 HOH HOH . E 4 HOH A 94 494 99 HOH HOH . E 4 HOH A 95 495 100 HOH HOH . E 4 HOH A 96 496 101 HOH HOH . E 4 HOH A 97 497 102 HOH HOH . E 4 HOH A 98 498 103 HOH HOH . E 4 HOH A 99 499 104 HOH HOH . E 4 HOH A 100 500 105 HOH HOH . E 4 HOH A 101 501 106 HOH HOH . E 4 HOH A 102 502 107 HOH HOH . E 4 HOH A 103 503 108 HOH HOH . E 4 HOH A 104 504 109 HOH HOH . E 4 HOH A 105 505 110 HOH HOH . E 4 HOH A 106 506 111 HOH HOH . E 4 HOH A 107 507 112 HOH HOH . E 4 HOH A 108 508 113 HOH HOH . E 4 HOH A 109 509 114 HOH HOH . E 4 HOH A 110 510 115 HOH HOH . E 4 HOH A 111 511 116 HOH HOH . E 4 HOH A 112 512 117 HOH HOH . E 4 HOH A 113 513 118 HOH HOH . E 4 HOH A 114 514 119 HOH HOH . E 4 HOH A 115 515 120 HOH HOH . E 4 HOH A 116 516 122 HOH HOH . E 4 HOH A 117 517 124 HOH HOH . E 4 HOH A 118 518 128 HOH HOH . E 4 HOH A 119 519 129 HOH HOH . E 4 HOH A 120 520 131 HOH HOH . E 4 HOH A 121 521 132 HOH HOH . E 4 HOH A 122 522 133 HOH HOH . E 4 HOH A 123 523 134 HOH HOH . E 4 HOH A 124 524 135 HOH HOH . E 4 HOH A 125 525 136 HOH HOH . E 4 HOH A 126 526 137 HOH HOH . E 4 HOH A 127 527 138 HOH HOH . E 4 HOH A 128 528 139 HOH HOH . E 4 HOH A 129 529 140 HOH HOH . E 4 HOH A 130 530 141 HOH HOH . E 4 HOH A 131 531 142 HOH HOH . E 4 HOH A 132 532 143 HOH HOH . E 4 HOH A 133 533 144 HOH HOH . E 4 HOH A 134 534 145 HOH HOH . E 4 HOH A 135 535 146 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 DUN . . . D 3 -1.536 19.417 20.977 1 11.32 ? N1 DUN 303 A 1 HETATM 2 C C2 DUN . . . D 3 -0.467 19.411 20.179 1 12.73 ? C2 DUN 303 A 1 HETATM 3 N N3 DUN . . . D 3 0.759 19.741 20.636 1 9.09 ? N3 DUN 303 A 1 HETATM 4 C C4 DUN . . . D 3 0.943 20.132 21.903 1 9.48 ? C4 DUN 303 A 1 HETATM 5 C C5 DUN . . . D 3 -0.14 20.163 22.754 1 9.4 ? C5 DUN 303 A 1 HETATM 6 C C6 DUN . . . D 3 -1.373 19.809 22.241 1 9.39 ? C6 DUN 303 A 1 HETATM 7 O O2 DUN . . . D 3 -0.588 19.044 18.92 1 10.43 ? O2 DUN 303 A 1 HETATM 8 O O4 DUN . . . D 3 2.178 20.459 22.355 1 9.78 ? O4 DUN 303 A 1 HETATM 9 C C1' DUN . . . D 3 -2.885 19.077 20.393 1 11.42 ? C1' DUN 303 A 1 HETATM 10 C C2' DUN . . . D 3 -3.062 17.649 19.914 1 9.59 ? C2' DUN 303 A 1 HETATM 11 C C3' DUN . . . D 3 -4.529 17.328 20.129 1 10.45 ? C3' DUN 303 A 1 HETATM 12 C C4' DUN . . . D 3 -5.042 18.508 20.959 1 8.8 ? C4' DUN 303 A 1 HETATM 13 O O4' DUN . . . D 3 -3.898 19.262 21.368 1 11.1 ? O4' DUN 303 A 1 HETATM 14 O O3' DUN . . . D 3 -5.169 17.309 18.84 1 7.64 ? O3' DUN 303 A 1 HETATM 15 C C5' DUN . . . D 3 -5.781 18.042 22.203 1 10.67 ? C5' DUN 303 A 1 HETATM 16 O O5' DUN . . . D 3 -6.241 19.177 22.924 1 11.01 ? O5' DUN 303 A 1 HETATM 17 P PA DUN . . . D 3 -7.21 19.06 24.184 1 11.48 ? PA DUN 303 A 1 HETATM 18 O O1A DUN . . . D 3 -6.988 20.346 24.921 1 11.74 ? O1A DUN 303 A 1 HETATM 19 O O2A DUN . . . D 3 -6.962 17.792 24.918 1 10.26 ? O2A DUN 303 A 1 HETATM 20 P PB DUN . . . D 3 -9.577 18.051 22.689 1 13.55 ? PB DUN 303 A 1 HETATM 21 O O1B DUN . . . D 3 -11.016 18.321 22.888 1 20.01 ? O1B DUN 303 A 1 HETATM 22 O O2B DUN . . . D 3 -9.16 18.366 21.287 1 22.24 ? O2B DUN 303 A 1 HETATM 23 O O3B DUN . . . D 3 -9.177 16.641 23.137 1 13.58 ? O3B DUN 303 A 1 HETATM 24 N N3A DUN . . . D 3 -8.796 19.172 23.654 1 10.04 ? N3A DUN 303 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 24 #