data_4WMB # _model_server_result.job_id CR7T-TXqaYr7AZbE3Twk4g _model_server_result.datetime_utc '2024-12-26 18:51:35' _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 4wmb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 4WMB # _exptl.entry_id 4WMB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 5 _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 90 _cell.angle_gamma 120 _cell.entry_id 4WMB _cell.length_a 89.468 _cell.length_b 89.468 _cell.length_c 42.934 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WMB _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 3' # _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,G,H _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 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 XYS _pdbx_entity_branch_link.comp_id_2 BGC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O3 _pdbx_entity_branch_link.leaving_atom_id_2 HO3 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 3 n C BGC 1 B 1 BGC E 1 GCX 3 n C XYS 2 B 2 XYS E 1 GCX # 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 263 A CYS 349 1_555 A SG CYS 288 A CYS 374 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 270 A CYS 356 1_555 A SG CYS 299 A CYS 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf3 B SG CYS 9 D CYS 51 1_555 B SG CYS 20 D CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf4 B SG CYS 14 D CYS 56 1_555 B SG CYS 29 D CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 B SG CYS 31 D CYS 73 1_555 B SG CYS 40 D CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 B OG SER 11 D SER 53 1_555 C C1 BGC . B BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.618 sing covale ? covale2 C O3 BGC . B BGC 1 1_555 C C1 XYS . B XYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 sing metalc ? metalc1 A OD2 ASP 139 A ASP 225 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc2 A OD1 ASP 141 A ASP 227 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc3 A OD2 ASP 141 A ASP 227 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc4 A NE2 HIS 296 A HIS 382 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc5 D MN MN . A MN 401 1_555 E O1A UDP . A UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc6 D MN MN . A MN 401 1_555 E O3B UDP . A UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? # _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 386 n n N1 C6 UDP sing 387 n n N1 C1' UDP sing 388 n n C2 N3 UDP sing 389 n n C2 O2 UDP doub 390 n n N3 C4 UDP sing 391 n n N3 HN3 UDP sing 392 n n C4 C5 UDP sing 393 n n C4 O4 UDP doub 394 n n C5 C6 UDP doub 395 n n C5 H5 UDP sing 396 n n C6 H6 UDP sing 397 n n C1' C2' UDP sing 398 n n C1' O4' UDP sing 399 n n C1' H1' UDP sing 400 n n C2' O2' UDP sing 401 n n C2' C3' UDP sing 402 n n C2' H2' UDP sing 403 n n O2' HO2' UDP sing 404 n n C3' C4' UDP sing 405 n n C3' O3' UDP sing 406 n n C3' H3' UDP sing 407 n n C4' O4' UDP sing 408 n n C4' C5' UDP sing 409 n n C4' H4' UDP sing 410 n n O3' HO3' UDP sing 411 n n C5' O5' UDP sing 412 n n C5' "H5'1" UDP sing 413 n n C5' "H5'2" UDP sing 414 n n O5' PA UDP sing 415 n n PA O1A UDP doub 416 n n PA O2A UDP sing 417 n n PA O3A UDP sing 418 n n O2A HOA2 UDP sing 419 n n O3A PB UDP sing 420 n n PB O1B UDP doub 421 n n PB O2B UDP sing 422 n n PB O3B UDP sing 423 n n O2B HOB2 UDP sing 424 n n O3B HOB3 UDP sing 425 n n # _atom_sites.entry_id 4WMB _atom_sites.fract_transf_matrix[1][1] 0.011177 _atom_sites.fract_transf_matrix[1][2] 0.006453 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012906 _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] 0.023292 _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 MN A 1 401 1 MN MN . E 5 UDP A 1 402 1 UDP UDP . F 6 SO4 A 1 403 1 SO4 SO4 . G 7 HOH A 1 501 52 HOH HOH . G 7 HOH A 2 502 57 HOH HOH . G 7 HOH A 3 503 12 HOH HOH . G 7 HOH A 4 504 8 HOH HOH . G 7 HOH A 5 505 62 HOH HOH . G 7 HOH A 6 506 1 HOH HOH . G 7 HOH A 7 507 61 HOH HOH . G 7 HOH A 8 508 7 HOH HOH . G 7 HOH A 9 509 36 HOH HOH . G 7 HOH A 10 510 58 HOH HOH . G 7 HOH A 11 511 3 HOH HOH . G 7 HOH A 12 512 4 HOH HOH . G 7 HOH A 13 513 5 HOH HOH . G 7 HOH A 14 514 6 HOH HOH . G 7 HOH A 15 515 9 HOH HOH . G 7 HOH A 16 516 11 HOH HOH . G 7 HOH A 17 517 13 HOH HOH . G 7 HOH A 18 518 14 HOH HOH . G 7 HOH A 19 519 15 HOH HOH . G 7 HOH A 20 520 16 HOH HOH . G 7 HOH A 21 521 17 HOH HOH . G 7 HOH A 22 522 18 HOH HOH . G 7 HOH A 23 523 19 HOH HOH . G 7 HOH A 24 524 20 HOH HOH . G 7 HOH A 25 525 21 HOH HOH . G 7 HOH A 26 526 23 HOH HOH . G 7 HOH A 27 527 24 HOH HOH . G 7 HOH A 28 528 25 HOH HOH . G 7 HOH A 29 529 26 HOH HOH . G 7 HOH A 30 530 27 HOH HOH . G 7 HOH A 31 531 29 HOH HOH . G 7 HOH A 32 532 30 HOH HOH . G 7 HOH A 33 533 31 HOH HOH . G 7 HOH A 34 534 32 HOH HOH . G 7 HOH A 35 535 34 HOH HOH . G 7 HOH A 36 536 35 HOH HOH . G 7 HOH A 37 537 37 HOH HOH . G 7 HOH A 38 538 38 HOH HOH . G 7 HOH A 39 539 39 HOH HOH . G 7 HOH A 40 540 40 HOH HOH . G 7 HOH A 41 541 41 HOH HOH . G 7 HOH A 42 542 42 HOH HOH . G 7 HOH A 43 543 43 HOH HOH . G 7 HOH A 44 544 44 HOH HOH . G 7 HOH A 45 545 45 HOH HOH . G 7 HOH A 46 546 46 HOH HOH . G 7 HOH A 47 547 48 HOH HOH . G 7 HOH A 48 548 49 HOH HOH . G 7 HOH A 49 549 50 HOH HOH . G 7 HOH A 50 550 51 HOH HOH . G 7 HOH A 51 551 53 HOH HOH . G 7 HOH A 52 552 54 HOH HOH . G 7 HOH A 53 553 55 HOH HOH . G 7 HOH A 54 554 56 HOH HOH . G 7 HOH A 55 555 59 HOH HOH . G 7 HOH A 56 556 60 HOH HOH . G 7 HOH A 57 557 63 HOH HOH . G 7 HOH A 58 558 64 HOH HOH . G 7 HOH A 59 559 65 HOH HOH . G 7 HOH A 60 560 67 HOH HOH . G 7 HOH A 61 561 68 HOH HOH . G 7 HOH A 62 562 69 HOH HOH . G 7 HOH A 63 563 70 HOH HOH . G 7 HOH A 64 564 71 HOH HOH . G 7 HOH A 65 565 72 HOH HOH . H 7 HOH D 1 201 2 HOH HOH . H 7 HOH D 2 202 10 HOH HOH . H 7 HOH D 3 203 22 HOH HOH . H 7 HOH D 4 204 28 HOH HOH . H 7 HOH D 5 205 33 HOH HOH . H 7 HOH D 6 206 66 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 . . . E 5 34.056 10.373 9.2 1 34.34 ? N1 UDP 402 A 1 HETATM 2 C C2 UDP . . . E 5 35.347 10.733 9.629 1 33 ? C2 UDP 402 A 1 HETATM 3 N N3 UDP . . . E 5 35.508 11.694 10.549 1 34.25 ? N3 UDP 402 A 1 HETATM 4 C C4 UDP . . . E 5 34.447 12.324 11.07 1 35.3 ? C4 UDP 402 A 1 HETATM 5 C C5 UDP . . . E 5 33.153 11.996 10.672 1 35.51 ? C5 UDP 402 A 1 HETATM 6 C C6 UDP . . . E 5 32.983 11.008 9.711 1 35.73 ? C6 UDP 402 A 1 HETATM 7 O O2 UDP . . . E 5 36.339 10.16 9.139 1 33.79 ? O2 UDP 402 A 1 HETATM 8 O O4 UDP . . . E 5 34.627 13.21 11.925 1 36.02 ? O4 UDP 402 A 1 HETATM 9 C C1' UDP . . . E 5 33.915 9.325 8.169 1 33.43 ? C1' UDP 402 A 1 HETATM 10 C C2' UDP . . . E 5 33.763 7.941 8.751 1 32.53 ? C2' UDP 402 A 1 HETATM 11 O O2' UDP . . . E 5 34.405 7.046 7.834 1 31.99 ? O2' UDP 402 A 1 HETATM 12 C C3' UDP . . . E 5 32.253 7.733 8.744 1 32.23 ? C3' UDP 402 A 1 HETATM 13 C C4' UDP . . . E 5 31.814 8.479 7.485 1 32.21 ? C4' UDP 402 A 1 HETATM 14 O O4' UDP . . . E 5 32.744 9.554 7.383 1 34.09 ? O4' UDP 402 A 1 HETATM 15 O O3' UDP . . . E 5 31.878 6.355 8.7 1 30.35 ? O3' UDP 402 A 1 HETATM 16 C C5' UDP . . . E 5 30.395 9.045 7.504 1 31.89 ? C5' UDP 402 A 1 HETATM 17 O O5' UDP . . . E 5 30.076 9.528 8.81 1 33.44 ? O5' UDP 402 A 1 HETATM 18 P PA UDP . . . E 5 29.114 8.674 9.756 1 33.03 ? PA UDP 402 A 1 HETATM 19 O O1A UDP . . . E 5 29.292 7.22 9.423 1 32.78 ? O1A UDP 402 A 1 HETATM 20 O O2A UDP . . . E 5 29.255 9.101 11.186 1 35.29 ? O2A UDP 402 A 1 HETATM 21 O O3A UDP . . . E 5 27.693 9.241 9.207 1 31.37 ? O3A UDP 402 A 1 HETATM 22 P PB UDP . . . E 5 26.338 8.377 9.038 1 33.62 ? PB UDP 402 A 1 HETATM 23 O O1B UDP . . . E 5 25.626 9.125 7.938 1 34.96 ? O1B UDP 402 A 1 HETATM 24 O O2B UDP . . . E 5 25.618 8.482 10.343 1 33.94 ? O2B UDP 402 A 1 HETATM 25 O O3B UDP . . . E 5 26.77 6.962 8.664 1 30.27 ? O3B UDP 402 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #