data_4WNH # _model_server_result.job_id 2IPrUjCza4e-6SowJUokmQ _model_server_result.datetime_utc '2024-11-08 20:45:11' _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 4wnh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 4WNH # _exptl.entry_id 4WNH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 536.276 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE" _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 4WNH _cell.length_a 89.481 _cell.length_b 89.481 _cell.length_c 42.895 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WNH _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 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 A SG CYS 270 A CYS 356 1_555 A SG CYS 299 A CYS 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf3 B SG CYS 9 D CYS 51 1_555 B SG CYS 20 D CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf4 B SG CYS 14 D CYS 56 1_555 B SG CYS 29 D CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 B SG CYS 31 D CYS 73 1_555 B SG CYS 40 D CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? covale ? covale1 B OG SER 11 D SER 53 1_555 C C1 BGC . B BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 C O3 BGC . B BGC 1 1_555 C C1 XYS . B XYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 sing metalc ? metalc1 A OD2 ASP 139 A ASP 225 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc2 A OD1 ASP 141 A ASP 227 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc3 A OD2 ASP 141 A ASP 227 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc4 A NE2 HIS 296 A HIS 382 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc5 D MN MN . A MN 401 1_555 E O2A UDX . A UDX 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc6 D MN MN . A MN 401 1_555 E O2B UDX . A UDX 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.838 ? # _chem_comp.formula 'C14 H22 N2 O16 P2' _chem_comp.formula_weight 536.276 _chem_comp.id UDX _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms UDP-ALPHA-D-XYLOPYRANOSE # 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 C1' C2' UDX sing 382 n n C1' O5' UDX sing 383 n n C1' O3B UDX sing 384 n n C1' H1' UDX sing 385 n n C2' O2' UDX sing 386 n n C2' C3' UDX sing 387 n n C2' "H2'1" UDX sing 388 n n O2' "HO'2" UDX sing 389 n n C3' O3' UDX sing 390 n n C3' C4' UDX sing 391 n n C3' "H3'1" UDX sing 392 n n O3' "HO'3" UDX sing 393 n n C4' O4' UDX sing 394 n n C4' C5' UDX sing 395 n n C4' "H4'1" UDX sing 396 n n O4' "HO'4" UDX sing 397 n n C5' O5' UDX sing 398 n n C5' "H5'1" UDX sing 399 n n C5' "H5'2" UDX sing 400 n n PB O1B UDX doub 401 n n PB O2B UDX sing 402 n n PB O3B UDX sing 403 n n PB O3A UDX sing 404 n n O2B HOB2 UDX sing 405 n n O3A PA UDX sing 406 n n PA O1A UDX doub 407 n n PA O2A UDX sing 408 n n PA O5D UDX sing 409 n n O2A HOA2 UDX sing 410 n n O5D C5D UDX sing 411 n n C5D C4D UDX sing 412 n n C5D H5A1 UDX sing 413 n n C5D H5A2 UDX sing 414 n n C4D O4D UDX sing 415 n n C4D C3D UDX sing 416 n n C4D H4A1 UDX sing 417 n n O4D C1D UDX sing 418 n n C3D O3D UDX sing 419 n n C3D C2D UDX sing 420 n n C3D H3A1 UDX sing 421 n n O3D HOA3 UDX sing 422 n n C2D O2D UDX sing 423 n n C2D C1D UDX sing 424 n n C2D H2A1 UDX sing 425 n n O2D HOC2 UDX sing 426 n n C1D N1 UDX sing 427 n n C1D "H1'1" UDX sing 428 n n N1 C6 UDX sing 429 n n N1 C2 UDX sing 430 n n C6 C5 UDX doub 431 n n C6 H61 UDX sing 432 n n C2 O2 UDX doub 433 n n C2 N3 UDX sing 434 n n N3 C4 UDX sing 435 n n N3 HN3 UDX sing 436 n n C4 O4 UDX doub 437 n n C4 C5 UDX sing 438 n n C5 H51 UDX sing 439 n n # _atom_sites.entry_id 4WNH _atom_sites.fract_transf_matrix[1][1] 0.011176 _atom_sites.fract_transf_matrix[1][2] 0.006452 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012904 _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] 0.023313 _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 UDX A 1 402 1 UDX UDX . F 6 HOH A 1 501 83 HOH HOH . F 6 HOH A 2 502 31 HOH HOH . F 6 HOH A 3 503 80 HOH HOH . F 6 HOH A 4 504 16 HOH HOH . F 6 HOH A 5 505 10 HOH HOH . F 6 HOH A 6 506 1 HOH HOH . F 6 HOH A 7 507 40 HOH HOH . F 6 HOH A 8 508 15 HOH HOH . F 6 HOH A 9 509 89 HOH HOH . F 6 HOH A 10 510 51 HOH HOH . F 6 HOH A 11 511 42 HOH HOH . F 6 HOH A 12 512 23 HOH HOH . F 6 HOH A 13 513 2 HOH HOH . F 6 HOH A 14 514 74 HOH HOH . F 6 HOH A 15 515 75 HOH HOH . F 6 HOH A 16 516 3 HOH HOH . F 6 HOH A 17 517 4 HOH HOH . F 6 HOH A 18 518 5 HOH HOH . F 6 HOH A 19 519 6 HOH HOH . F 6 HOH A 20 520 7 HOH HOH . F 6 HOH A 21 521 8 HOH HOH . F 6 HOH A 22 522 9 HOH HOH . F 6 HOH A 23 523 11 HOH HOH . F 6 HOH A 24 524 13 HOH HOH . F 6 HOH A 25 525 14 HOH HOH . F 6 HOH A 26 526 17 HOH HOH . F 6 HOH A 27 527 18 HOH HOH . F 6 HOH A 28 528 19 HOH HOH . F 6 HOH A 29 529 20 HOH HOH . F 6 HOH A 30 530 21 HOH HOH . F 6 HOH A 31 531 22 HOH HOH . F 6 HOH A 32 532 24 HOH HOH . F 6 HOH A 33 533 25 HOH HOH . F 6 HOH A 34 534 26 HOH HOH . F 6 HOH A 35 535 27 HOH HOH . F 6 HOH A 36 536 28 HOH HOH . F 6 HOH A 37 537 29 HOH HOH . F 6 HOH A 38 538 30 HOH HOH . F 6 HOH A 39 539 32 HOH HOH . F 6 HOH A 40 540 34 HOH HOH . F 6 HOH A 41 541 35 HOH HOH . F 6 HOH A 42 542 36 HOH HOH . F 6 HOH A 43 543 37 HOH HOH . F 6 HOH A 44 544 38 HOH HOH . F 6 HOH A 45 545 39 HOH HOH . F 6 HOH A 46 546 43 HOH HOH . F 6 HOH A 47 547 44 HOH HOH . F 6 HOH A 48 548 45 HOH HOH . F 6 HOH A 49 549 47 HOH HOH . F 6 HOH A 50 550 48 HOH HOH . F 6 HOH A 51 551 49 HOH HOH . F 6 HOH A 52 552 50 HOH HOH . F 6 HOH A 53 553 52 HOH HOH . F 6 HOH A 54 554 53 HOH HOH . F 6 HOH A 55 555 56 HOH HOH . F 6 HOH A 56 556 57 HOH HOH . F 6 HOH A 57 557 58 HOH HOH . F 6 HOH A 58 558 59 HOH HOH . F 6 HOH A 59 559 60 HOH HOH . F 6 HOH A 60 560 61 HOH HOH . F 6 HOH A 61 561 62 HOH HOH . F 6 HOH A 62 562 63 HOH HOH . F 6 HOH A 63 563 64 HOH HOH . F 6 HOH A 64 564 65 HOH HOH . F 6 HOH A 65 565 66 HOH HOH . F 6 HOH A 66 566 67 HOH HOH . F 6 HOH A 67 567 68 HOH HOH . F 6 HOH A 68 568 69 HOH HOH . F 6 HOH A 69 569 70 HOH HOH . F 6 HOH A 70 570 71 HOH HOH . F 6 HOH A 71 571 72 HOH HOH . F 6 HOH A 72 572 73 HOH HOH . F 6 HOH A 73 573 77 HOH HOH . F 6 HOH A 74 574 78 HOH HOH . F 6 HOH A 75 575 81 HOH HOH . F 6 HOH A 76 576 82 HOH HOH . F 6 HOH A 77 577 84 HOH HOH . F 6 HOH A 78 578 85 HOH HOH . F 6 HOH A 79 579 88 HOH HOH . F 6 HOH A 80 580 90 HOH HOH . G 6 HOH D 1 201 12 HOH HOH . G 6 HOH D 2 202 33 HOH HOH . G 6 HOH D 3 203 41 HOH HOH . G 6 HOH D 4 204 46 HOH HOH . G 6 HOH D 5 205 55 HOH HOH . G 6 HOH D 6 206 76 HOH HOH . G 6 HOH D 7 207 79 HOH HOH . G 6 HOH D 8 208 86 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 C C1' UDX . . . E 5 -23.335 8.836 7.233 0.9 35.08 ? C1' UDX 402 A 1 HETATM 2 C C2' UDX . . . E 5 -23.485 9.018 5.71 0.9 35.65 ? C2' UDX 402 A 1 HETATM 3 O O2' UDX . . . E 5 -24.865 8.807 5.322 0.9 35.05 ? O2' UDX 402 A 1 HETATM 4 C C3' UDX . . . E 5 -22.476 8.111 4.975 0.9 37.17 ? C3' UDX 402 A 1 HETATM 5 O O3' UDX . . . E 5 -22.428 8.259 3.539 0.9 34.26 ? O3' UDX 402 A 1 HETATM 6 C C4' UDX . . . E 5 -21.067 8.447 5.483 0.9 37.93 ? C4' UDX 402 A 1 HETATM 7 O O4' UDX . . . E 5 -20.087 7.628 4.816 0.9 36.35 ? O4' UDX 402 A 1 HETATM 8 C C5' UDX . . . E 5 -20.982 8.292 7.007 0.9 37.27 ? C5' UDX 402 A 1 HETATM 9 O O5' UDX . . . E 5 -21.981 9.103 7.647 0.9 35.21 ? O5' UDX 402 A 1 HETATM 10 P PB UDX . . . E 5 -24.346 7.017 8.988 0.9 31.78 ? PB UDX 402 A 1 HETATM 11 O O1B UDX . . . E 5 -24.621 8.162 9.948 0.9 26.09 ? O1B UDX 402 A 1 HETATM 12 O O2B UDX . . . E 5 -25.399 5.975 8.632 0.9 26.14 ? O2B UDX 402 A 1 HETATM 13 O O3B UDX . . . E 5 -23.737 7.505 7.578 0.9 34.21 ? O3B UDX 402 A 1 HETATM 14 O O3A UDX . . . E 5 -23.005 6.378 9.584 0.9 31.96 ? O3A UDX 402 A 1 HETATM 15 P PA UDX . . . E 5 -22.724 4.832 9.901 0.9 32.2 ? PA UDX 402 A 1 HETATM 16 O O1A UDX . . . E 5 -22.289 4.759 11.346 0.9 35.57 ? O1A UDX 402 A 1 HETATM 17 O O2A UDX . . . E 5 -23.801 3.938 9.38 0.9 29.9 ? O2A UDX 402 A 1 HETATM 18 O O5D UDX . . . E 5 -21.454 4.617 8.947 0.9 31.84 ? O5D UDX 402 A 1 HETATM 19 C C5D UDX . . . E 5 -21.601 4.087 7.62 0.9 30.78 ? C5D UDX 402 A 1 HETATM 20 C C4D UDX . . . E 5 -21.477 2.561 7.553 0.9 30.26 ? C4D UDX 402 A 1 HETATM 21 O O4D UDX . . . E 5 -20.106 2.217 7.332 0.9 31.13 ? O4D UDX 402 A 1 HETATM 22 C C3D UDX . . . E 5 -21.888 1.745 8.783 0.9 29.53 ? C3D UDX 402 A 1 HETATM 23 O O3D UDX . . . E 5 -23.257 1.347 8.732 0.9 26.37 ? O3D UDX 402 A 1 HETATM 24 C C2D UDX . . . E 5 -20.972 0.534 8.731 0.9 30.49 ? C2D UDX 402 A 1 HETATM 25 O O2D UDX . . . E 5 -21.476 -0.502 7.863 0.9 31.42 ? O2D UDX 402 A 1 HETATM 26 C C1D UDX . . . E 5 -19.708 1.093 8.123 0.9 30.74 ? C1D UDX 402 A 1 HETATM 27 N N1 UDX . . . E 5 -18.72 1.496 9.133 0.9 31.08 ? N1 UDX 402 A 1 HETATM 28 C C6 UDX . . . E 5 -18.698 2.742 9.626 0.9 32.35 ? C6 UDX 402 A 1 HETATM 29 C C2 UDX . . . E 5 -17.736 0.569 9.56 0.9 31.11 ? C2 UDX 402 A 1 HETATM 30 O O2 UDX . . . E 5 -17.705 -0.59 9.11 0.9 29.46 ? O2 UDX 402 A 1 HETATM 31 N N3 UDX . . . E 5 -16.811 0.927 10.472 0.9 31.54 ? N3 UDX 402 A 1 HETATM 32 C C4 UDX . . . E 5 -16.803 2.176 10.968 0.9 31.54 ? C4 UDX 402 A 1 HETATM 33 O O4 UDX . . . E 5 -15.936 2.482 11.789 0.9 32.2 ? O4 UDX 402 A 1 HETATM 34 C C5 UDX . . . E 5 -17.743 3.106 10.564 0.9 32.17 ? C5 UDX 402 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 34 #