data_7JHN # _model_server_result.job_id VkEeCd7Jk8_OqEf-BEEmqw _model_server_result.datetime_utc '2025-07-08 01:21:37' _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 7jhn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":403}' # _entry.id 7JHN # _exptl.entry_id 7JHN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-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 105.82 _cell.angle_gamma 90 _cell.entry_id 7JHN _cell.length_a 82.916 _cell.length_b 76.865 _cell.length_c 66.786 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7JHN _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 3 2 1 GAL NAG C1 O1 . O4 HO4 . sing 6 ? 3 3 2 NAG GAL C1 O1 . O3 HO3 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 402 NAG 2 n B NAG 2 B 2 NAG A 403 NAG 2 n B BMA 3 B 3 BMA A 404 BMA 2 n B MAN 4 B 4 MAN A 405 MAN 2 n B MAN 5 B 5 MAN A 406 MAN 3 n C NAG 1 C 1 NAG A 413 LIG 3 n C GAL 2 C 2 GAL A 413 LIG 3 n C NAG 3 C 3 NAG A 413 LIG # 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 disulf ? disulf1 A SG CYS 69 A CYS 96 1_555 A SG CYS 98 A CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 111 A CYS 138 1_555 A SG CYS 208 A CYS 235 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 340 A CYS 367 1_555 A SG CYS 370 A CYS 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 100 A ASN 127 1_555 D C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale2 A ND2 ASN 192 A ASN 219 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale5 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale6 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale8 C O3 GAL . C GAL 2 1_555 C C1 NAG . C NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? metalc ? metalc1 A OD1 ASP 220 A ASP 247 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.913 ? metalc ? metalc2 A OD2 ASP 220 A ASP 247 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc3 E MG MG . A MG 402 1_555 F O2A UDP . A UDP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc4 E MG MG . A MG 402 1_555 F O3B UDP . A UDP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc5 E MG MG . A MG 402 1_555 I O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc6 E MG MG . A MG 402 1_555 I O HOH . A HOH 557 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # 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 UDP sing 460 n n N1 C6 UDP sing 461 n n N1 C1' UDP sing 462 n n C2 N3 UDP sing 463 n n C2 O2 UDP doub 464 n n N3 C4 UDP sing 465 n n N3 HN3 UDP sing 466 n n C4 C5 UDP sing 467 n n C4 O4 UDP doub 468 n n C5 C6 UDP doub 469 n n C5 H5 UDP sing 470 n n C6 H6 UDP sing 471 n n C1' C2' UDP sing 472 n n C1' O4' UDP sing 473 n n C1' H1' UDP sing 474 n n C2' O2' UDP sing 475 n n C2' C3' UDP sing 476 n n C2' H2' UDP sing 477 n n O2' HO2' UDP sing 478 n n C3' C4' UDP sing 479 n n C3' O3' UDP sing 480 n n C3' H3' UDP sing 481 n n C4' O4' UDP sing 482 n n C4' C5' UDP sing 483 n n C4' H4' UDP sing 484 n n O3' HO3' UDP sing 485 n n C5' O5' UDP sing 486 n n C5' "H5'1" UDP sing 487 n n C5' "H5'2" UDP sing 488 n n O5' PA UDP sing 489 n n PA O1A UDP doub 490 n n PA O2A UDP sing 491 n n PA O3A UDP sing 492 n n O2A HOA2 UDP sing 493 n n O3A PB UDP sing 494 n n PB O1B UDP doub 495 n n PB O2B UDP sing 496 n n PB O3B UDP sing 497 n n O2B HOB2 UDP sing 498 n n O3B HOB3 UDP sing 499 n n # _atom_sites.entry_id 7JHN _atom_sites.fract_transf_matrix[1][1] 0.01206 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003418 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01301 _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] 0.015563 _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 D 4 NAG A 1 401 401 NAG NAG . E 5 MG A 1 402 411 MG MG . F 6 UDP A 1 403 412 UDP UDP . G 7 CL A 1 404 1 CL CL . H 7 CL A 1 405 2 CL CL . I 8 HOH A 1 501 4 HOH HOH . I 8 HOH A 2 502 47 HOH HOH . I 8 HOH A 3 503 17 HOH HOH . I 8 HOH A 4 504 44 HOH HOH . I 8 HOH A 5 505 90 HOH HOH . I 8 HOH A 6 506 21 HOH HOH . I 8 HOH A 7 507 49 HOH HOH . I 8 HOH A 8 508 101 HOH HOH . I 8 HOH A 9 509 76 HOH HOH . I 8 HOH A 10 510 59 HOH HOH . I 8 HOH A 11 511 46 HOH HOH . I 8 HOH A 12 512 43 HOH HOH . I 8 HOH A 13 513 51 HOH HOH . I 8 HOH A 14 514 29 HOH HOH . I 8 HOH A 15 515 32 HOH HOH . I 8 HOH A 16 516 14 HOH HOH . I 8 HOH A 17 517 25 HOH HOH . I 8 HOH A 18 518 83 HOH HOH . I 8 HOH A 19 519 22 HOH HOH . I 8 HOH A 20 520 11 HOH HOH . I 8 HOH A 21 521 34 HOH HOH . I 8 HOH A 22 522 23 HOH HOH . I 8 HOH A 23 523 26 HOH HOH . I 8 HOH A 24 524 36 HOH HOH . I 8 HOH A 25 525 7 HOH HOH . I 8 HOH A 26 526 3 HOH HOH . I 8 HOH A 27 527 42 HOH HOH . I 8 HOH A 28 528 27 HOH HOH . I 8 HOH A 29 529 10 HOH HOH . I 8 HOH A 30 530 62 HOH HOH . I 8 HOH A 31 531 18 HOH HOH . I 8 HOH A 32 532 8 HOH HOH . I 8 HOH A 33 533 13 HOH HOH . I 8 HOH A 34 534 50 HOH HOH . I 8 HOH A 35 535 74 HOH HOH . I 8 HOH A 36 536 81 HOH HOH . I 8 HOH A 37 537 19 HOH HOH . I 8 HOH A 38 538 6 HOH HOH . I 8 HOH A 39 539 9 HOH HOH . I 8 HOH A 40 540 5 HOH HOH . I 8 HOH A 41 541 20 HOH HOH . I 8 HOH A 42 542 31 HOH HOH . I 8 HOH A 43 543 64 HOH HOH . I 8 HOH A 44 544 63 HOH HOH . I 8 HOH A 45 545 35 HOH HOH . I 8 HOH A 46 546 48 HOH HOH . I 8 HOH A 47 547 1 HOH HOH . I 8 HOH A 48 548 58 HOH HOH . I 8 HOH A 49 549 75 HOH HOH . I 8 HOH A 50 550 65 HOH HOH . I 8 HOH A 51 551 38 HOH HOH . I 8 HOH A 52 552 91 HOH HOH . I 8 HOH A 53 553 2 HOH HOH . I 8 HOH A 54 554 12 HOH HOH . I 8 HOH A 55 555 84 HOH HOH . I 8 HOH A 56 556 37 HOH HOH . I 8 HOH A 57 557 53 HOH HOH . I 8 HOH A 58 558 77 HOH HOH . I 8 HOH A 59 559 73 HOH HOH . I 8 HOH A 60 560 66 HOH HOH . I 8 HOH A 61 561 41 HOH HOH . I 8 HOH A 62 562 93 HOH HOH . I 8 HOH A 63 563 70 HOH HOH . I 8 HOH A 64 564 112 HOH HOH . I 8 HOH A 65 565 71 HOH HOH . I 8 HOH A 66 566 56 HOH HOH . I 8 HOH A 67 567 28 HOH HOH . I 8 HOH A 68 568 24 HOH HOH . I 8 HOH A 69 569 68 HOH HOH . I 8 HOH A 70 570 39 HOH HOH . I 8 HOH A 71 571 30 HOH HOH . I 8 HOH A 72 572 96 HOH HOH . I 8 HOH A 73 573 78 HOH HOH . I 8 HOH A 74 574 61 HOH HOH . I 8 HOH A 75 575 15 HOH HOH . I 8 HOH A 76 576 40 HOH HOH . I 8 HOH A 77 577 57 HOH HOH . I 8 HOH A 78 578 16 HOH HOH . I 8 HOH A 79 579 60 HOH HOH . I 8 HOH A 80 580 114 HOH HOH . I 8 HOH A 81 581 72 HOH HOH . I 8 HOH A 82 582 85 HOH HOH . I 8 HOH A 83 583 82 HOH HOH . I 8 HOH A 84 584 117 HOH HOH . I 8 HOH A 85 585 45 HOH HOH . I 8 HOH A 86 586 111 HOH HOH . I 8 HOH A 87 587 94 HOH HOH . I 8 HOH A 88 588 80 HOH HOH . I 8 HOH A 89 589 103 HOH HOH . I 8 HOH A 90 590 115 HOH HOH . I 8 HOH A 91 591 107 HOH HOH . I 8 HOH A 92 592 97 HOH HOH . I 8 HOH A 93 593 89 HOH HOH . I 8 HOH A 94 594 109 HOH HOH . I 8 HOH A 95 595 108 HOH HOH . I 8 HOH A 96 596 67 HOH HOH . I 8 HOH A 97 597 110 HOH HOH . I 8 HOH A 98 598 79 HOH HOH . I 8 HOH A 99 599 116 HOH HOH . I 8 HOH A 100 600 54 HOH HOH . I 8 HOH A 101 601 92 HOH HOH . I 8 HOH A 102 602 98 HOH HOH . I 8 HOH A 103 603 105 HOH HOH . I 8 HOH A 104 604 113 HOH HOH . I 8 HOH A 105 605 104 HOH HOH . I 8 HOH A 106 606 102 HOH HOH . I 8 HOH A 107 607 88 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 UDP . . . F 6 -17.294 0.031 23.292 1 25.2 ? N1 UDP 403 A 1 HETATM 2 C C2 UDP . . . F 6 -17.274 -1.067 22.459 1 24.85 ? C2 UDP 403 A 1 HETATM 3 N N3 UDP . . . F 6 -16.343 -1.145 21.443 1 23.91 ? N3 UDP 403 A 1 HETATM 4 C C4 UDP . . . F 6 -15.436 -0.119 21.266 1 22.6 ? C4 UDP 403 A 1 HETATM 5 C C5 UDP . . . F 6 -15.468 0.984 22.11 1 21.46 ? C5 UDP 403 A 1 HETATM 6 C C6 UDP . . . F 6 -16.502 1.11 23.028 1 16.34 ? C6 UDP 403 A 1 HETATM 7 O O2 UDP . . . F 6 -18.091 -1.971 22.629 1 20.68 ? O2 UDP 403 A 1 HETATM 8 O O4 UDP . . . F 6 -14.6 -0.179 20.366 1 26.69 ? O4 UDP 403 A 1 HETATM 9 C C1' UDP . . . F 6 -18.303 0.089 24.36 1 15.74 ? C1' UDP 403 A 1 HETATM 10 C C2' UDP . . . F 6 -17.66 0.376 25.705 1 18.08 ? C2' UDP 403 A 1 HETATM 11 O O2' UDP . . . F 6 -17.37 -0.803 26.418 1 21.8 ? O2' UDP 403 A 1 HETATM 12 C C3' UDP . . . F 6 -18.719 1.196 26.407 1 23.9 ? C3' UDP 403 A 1 HETATM 13 C C4' UDP . . . F 6 -19.534 1.829 25.289 1 21.46 ? C4' UDP 403 A 1 HETATM 14 O O4' UDP . . . F 6 -19.219 1.134 24.1 1 31.69 ? O4' UDP 403 A 1 HETATM 15 O O3' UDP . . . F 6 -19.533 0.322 27.149 1 19.16 ? O3' UDP 403 A 1 HETATM 16 C C5' UDP . . . F 6 -19.184 3.299 25.106 1 28.85 ? C5' UDP 403 A 1 HETATM 17 O O5' UDP . . . F 6 -17.792 3.41 25.29 1 36.25 ? O5' UDP 403 A 1 HETATM 18 P PA UDP . . . F 6 -17.13 4.72 25.939 1 32.67 ? PA UDP 403 A 1 HETATM 19 O O1A UDP . . . F 6 -15.675 4.769 25.677 1 36.52 ? O1A UDP 403 A 1 HETATM 20 O O2A UDP . . . F 6 -17.401 4.713 27.395 1 45.53 ? O2A UDP 403 A 1 HETATM 21 O O3A UDP . . . F 6 -17.898 5.941 25.222 1 44.63 ? O3A UDP 403 A 1 HETATM 22 P PB UDP . . . F 6 -18.522 7.167 26.059 1 52.25 ? PB UDP 403 A 1 HETATM 23 O O1B UDP . . . F 6 -19.272 8.053 25.14 1 61.56 ? O1B UDP 403 A 1 HETATM 24 O O2B UDP . . . F 6 -17.421 7.929 26.691 1 54.85 ? O2B UDP 403 A 1 HETATM 25 O O3B UDP . . . F 6 -19.42 6.641 27.112 1 54.33 ? O3B UDP 403 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 25 #