data_4LW6 # _model_server_result.job_id X_JZDKKlIauwxPJRrnNA9g _model_server_result.datetime_utc '2024-11-14 16:29:14' _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 4lw6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 4LW6 # _exptl.entry_id 4LW6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 4 _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 90 _cell.entry_id 4LW6 _cell.length_a 81.943 _cell.length_b 81.943 _cell.length_c 133.053 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LW6 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 XYP _pdbx_entity_branch_link.comp_id_2 XYP _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 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _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 2 n B XYP 1 B 1 XYP A 564 XYP 2 n B XYP 2 B 2 XYP A 563 XYP # 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 231 A CYS 255 1_555 A SG CYS 286 A CYS 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf2 A SG CYS 276 A CYS 300 1_555 A SG CYS 284 A CYS 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 B O4 XYP . B XYP 1 1_555 B C1 XYP . B XYP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? metalc ? metalc1 A OD2 ASP 123 A ASP 147 1_555 C MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc2 A NE2 HIS 217 A HIS 241 1_555 C MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc3 A ND1 HIS 219 A HIS 243 1_555 C MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc4 C MN MN . A MN 401 1_555 D O1B UDP . A UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc5 C MN MN . A MN 401 1_555 D O1A UDP . A UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc6 C MN MN . A MN 401 1_555 F O HOH . A HOH 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? # _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 372 n n N1 C6 UDP sing 373 n n N1 C1' UDP sing 374 n n C2 N3 UDP sing 375 n n C2 O2 UDP doub 376 n n N3 C4 UDP sing 377 n n N3 HN3 UDP sing 378 n n C4 C5 UDP sing 379 n n C4 O4 UDP doub 380 n n C5 C6 UDP doub 381 n n C5 H5 UDP sing 382 n n C6 H6 UDP sing 383 n n C1' C2' UDP sing 384 n n C1' O4' UDP sing 385 n n C1' H1' UDP sing 386 n n C2' O2' UDP sing 387 n n C2' C3' UDP sing 388 n n C2' H2' UDP sing 389 n n O2' HO2' UDP sing 390 n n C3' C4' UDP sing 391 n n C3' O3' UDP sing 392 n n C3' H3' UDP sing 393 n n C4' O4' UDP sing 394 n n C4' C5' UDP sing 395 n n C4' H4' UDP sing 396 n n O3' HO3' UDP sing 397 n n C5' O5' UDP sing 398 n n C5' "H5'1" UDP sing 399 n n C5' "H5'2" UDP sing 400 n n O5' PA UDP sing 401 n n PA O1A UDP doub 402 n n PA O2A UDP sing 403 n n PA O3A UDP sing 404 n n O2A HOA2 UDP sing 405 n n O3A PB UDP sing 406 n n PB O1B UDP doub 407 n n PB O2B UDP sing 408 n n PB O3B UDP sing 409 n n O2B HOB2 UDP sing 410 n n O3B HOB3 UDP sing 411 n n # _atom_sites.entry_id 4LW6 _atom_sites.fract_transf_matrix[1][1] 0.012204 _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] 0.012204 _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] 0.007516 _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 C 3 MN A 1 401 335 MN MN . D 4 UDP A 1 402 336 UDP UDP . E 5 SEL A 1 405 1 SEL SEL . F 6 HOH A 1 501 1 HOH HOH . F 6 HOH A 2 502 2 HOH HOH . F 6 HOH A 3 503 3 HOH HOH . F 6 HOH A 4 504 4 HOH HOH . F 6 HOH A 5 505 5 HOH HOH . F 6 HOH A 6 506 6 HOH HOH . F 6 HOH A 7 507 7 HOH HOH . F 6 HOH A 8 508 8 HOH HOH . F 6 HOH A 9 509 9 HOH HOH . F 6 HOH A 10 510 10 HOH HOH . F 6 HOH A 11 511 11 HOH HOH . F 6 HOH A 12 512 12 HOH HOH . F 6 HOH A 13 513 13 HOH HOH . F 6 HOH A 14 514 14 HOH HOH . F 6 HOH A 15 515 15 HOH HOH . F 6 HOH A 16 516 16 HOH HOH . F 6 HOH A 17 517 17 HOH HOH . F 6 HOH A 18 518 18 HOH HOH . F 6 HOH A 19 519 19 HOH HOH . F 6 HOH A 20 520 20 HOH HOH . F 6 HOH A 21 521 21 HOH HOH . F 6 HOH A 22 522 22 HOH HOH . F 6 HOH A 23 523 23 HOH HOH . F 6 HOH A 24 524 24 HOH HOH . F 6 HOH A 25 525 25 HOH HOH . F 6 HOH A 26 526 26 HOH HOH . F 6 HOH A 27 527 27 HOH HOH . F 6 HOH A 28 528 28 HOH HOH . F 6 HOH A 29 529 29 HOH HOH . F 6 HOH A 30 530 30 HOH HOH . F 6 HOH A 31 531 31 HOH HOH . F 6 HOH A 32 532 32 HOH HOH . F 6 HOH A 33 533 33 HOH HOH . F 6 HOH A 34 534 34 HOH HOH . F 6 HOH A 35 535 35 HOH HOH . F 6 HOH A 36 536 36 HOH HOH . F 6 HOH A 37 537 37 HOH HOH . F 6 HOH A 38 538 38 HOH HOH . F 6 HOH A 39 539 39 HOH HOH . F 6 HOH A 40 540 40 HOH HOH . F 6 HOH A 41 541 41 HOH HOH . F 6 HOH A 42 542 42 HOH HOH . F 6 HOH A 43 543 43 HOH HOH . F 6 HOH A 44 544 44 HOH HOH . F 6 HOH A 45 545 45 HOH HOH . F 6 HOH A 46 546 46 HOH HOH . F 6 HOH A 47 547 47 HOH HOH . F 6 HOH A 48 548 48 HOH HOH . F 6 HOH A 49 549 49 HOH HOH . F 6 HOH A 50 550 50 HOH HOH . F 6 HOH A 51 551 51 HOH HOH . F 6 HOH A 52 552 52 HOH HOH . F 6 HOH A 53 553 53 HOH HOH . F 6 HOH A 54 554 54 HOH HOH . F 6 HOH A 55 555 55 HOH HOH . F 6 HOH A 56 556 56 HOH HOH . F 6 HOH A 57 557 57 HOH HOH . F 6 HOH A 58 558 58 HOH HOH . F 6 HOH A 59 559 59 HOH HOH . F 6 HOH A 60 560 60 HOH HOH . F 6 HOH A 61 561 61 HOH HOH . F 6 HOH A 62 562 62 HOH HOH . F 6 HOH A 63 563 63 HOH HOH . F 6 HOH A 64 564 64 HOH HOH . F 6 HOH A 65 565 65 HOH HOH . F 6 HOH A 66 566 66 HOH HOH . F 6 HOH A 67 567 67 HOH HOH . F 6 HOH A 68 568 68 HOH HOH . F 6 HOH A 69 569 69 HOH HOH . F 6 HOH A 70 570 70 HOH HOH . F 6 HOH A 71 571 71 HOH HOH . F 6 HOH A 72 572 72 HOH HOH . F 6 HOH A 73 573 73 HOH HOH . F 6 HOH A 74 574 74 HOH HOH . F 6 HOH A 75 575 75 HOH HOH . F 6 HOH A 76 576 76 HOH HOH . F 6 HOH A 77 577 77 HOH HOH . F 6 HOH A 78 578 78 HOH HOH . F 6 HOH A 79 579 79 HOH HOH . F 6 HOH A 80 580 80 HOH HOH . F 6 HOH A 81 581 81 HOH HOH . F 6 HOH A 82 582 82 HOH HOH . F 6 HOH A 83 583 83 HOH HOH . F 6 HOH A 84 584 84 HOH HOH . F 6 HOH A 85 585 85 HOH HOH . F 6 HOH A 86 586 86 HOH HOH . F 6 HOH A 87 587 87 HOH HOH . F 6 HOH A 88 588 88 HOH HOH . F 6 HOH A 89 589 89 HOH HOH . F 6 HOH A 90 590 90 HOH HOH . F 6 HOH A 91 591 91 HOH HOH . F 6 HOH A 92 592 92 HOH HOH . F 6 HOH A 93 593 93 HOH HOH . F 6 HOH A 94 594 94 HOH HOH . F 6 HOH A 95 595 95 HOH HOH . F 6 HOH A 96 596 96 HOH HOH . F 6 HOH A 97 597 97 HOH HOH . F 6 HOH A 98 598 98 HOH HOH . F 6 HOH A 99 599 99 HOH HOH . F 6 HOH A 100 600 100 HOH HOH . F 6 HOH A 101 601 101 HOH HOH . F 6 HOH A 102 602 102 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 . . . D 4 20.358 25.254 9.396 1 48.32 ? N1 UDP 402 A 1 HETATM 2 C C2 UDP . . . D 4 20.139 24.941 8.058 1 44.99 ? C2 UDP 402 A 1 HETATM 3 N N3 UDP . . . D 4 20.775 25.661 7.062 1 44.97 ? N3 UDP 402 A 1 HETATM 4 C C4 UDP . . . D 4 21.631 26.684 7.405 1 46.73 ? C4 UDP 402 A 1 HETATM 5 C C5 UDP . . . D 4 21.856 26.999 8.755 1 42.93 ? C5 UDP 402 A 1 HETATM 6 C C6 UDP . . . D 4 21.331 26.164 9.733 1 43.98 ? C6 UDP 402 A 1 HETATM 7 O O2 UDP . . . D 4 19.374 24.024 7.736 1 42.31 ? O2 UDP 402 A 1 HETATM 8 O O4 UDP . . . D 4 22.171 27.33 6.495 1 44.19 ? O4 UDP 402 A 1 HETATM 9 C C1' UDP . . . D 4 19.644 24.497 10.455 1 46.98 ? C1' UDP 402 A 1 HETATM 10 C C2' UDP . . . D 4 20.169 23.08 10.691 1 46.04 ? C2' UDP 402 A 1 HETATM 11 O O2' UDP . . . D 4 19.077 22.266 11.164 1 43.58 ? O2' UDP 402 A 1 HETATM 12 C C3' UDP . . . D 4 21.205 23.38 11.766 1 45.97 ? C3' UDP 402 A 1 HETATM 13 C C4' UDP . . . D 4 20.383 24.339 12.647 1 46.43 ? C4' UDP 402 A 1 HETATM 14 O O4' UDP . . . D 4 19.815 25.199 11.674 1 47.95 ? O4' UDP 402 A 1 HETATM 15 O O3' UDP . . . D 4 21.749 22.227 12.409 1 42.85 ? O3' UDP 402 A 1 HETATM 16 C C5' UDP . . . D 4 21.174 25.165 13.629 1 42.4 ? C5' UDP 402 A 1 HETATM 17 O O5' UDP . . . D 4 22.214 25.678 12.834 1 50.66 ? O5' UDP 402 A 1 HETATM 18 P PA UDP . . . D 4 23.784 25.436 13.195 1 49.43 ? PA UDP 402 A 1 HETATM 19 O O1A UDP . . . D 4 24.182 24.032 12.912 1 47.17 ? O1A UDP 402 A 1 HETATM 20 O O2A UDP . . . D 4 24.629 26.38 12.442 1 47.69 ? O2A UDP 402 A 1 HETATM 21 O O3A UDP . . . D 4 23.815 25.714 14.799 1 57.11 ? O3A UDP 402 A 1 HETATM 22 P PB UDP . . . D 4 25.002 25.25 15.81 1 45.55 ? PB UDP 402 A 1 HETATM 23 O O1B UDP . . . D 4 25.788 24.105 15.275 1 45.19 ? O1B UDP 402 A 1 HETATM 24 O O2B UDP . . . D 4 25.919 26.421 15.988 1 42.61 ? O2B UDP 402 A 1 HETATM 25 O O3B UDP . . . D 4 24.341 24.868 17.102 1 51.18 ? O3B UDP 402 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #