data_5U84 # _model_server_result.job_id V37E0rRd8C0oA8-wcSkF5A _model_server_result.datetime_utc '2024-11-17 12:48:38' _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 5u84 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":426}' # _entry.id 5U84 # _exptl.entry_id 5U84 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 126.904 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'IODIDE ION' _entity.pdbx_number_of_molecules 34 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.97 _cell.angle_gamma 90 _cell.entry_id 5U84 _cell.length_a 118.815 _cell.length_b 109.267 _cell.length_c 79.541 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5U84 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,WA 1 1 B,E,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,XA 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 M N N ? 5 N N N ? 5 O N N ? 5 P N N ? 5 Q N N ? 5 R N N ? 5 S N N ? 5 T N N ? 5 U N N ? 5 V N N ? 5 W N N ? 5 X N N ? 5 Y N N ? 5 Z N N ? 5 AA N N ? 5 BA N N ? 5 CA N N ? 5 DA N N ? 5 GA N N ? 5 HA N N ? 5 IA N N ? 5 JA N N ? 5 KA N N ? 5 LA N N ? 5 MA N N ? 5 NA N N ? 5 OA N N ? 5 PA N N ? 5 QA N N ? 5 RA N N ? 5 SA N N ? 5 TA N N ? 5 UA N N ? 5 VA N 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 1 FUC NAG C1 O1 . O6 HO6 . sing 3 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . 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 C NAG 1 C 1 NAG C 1 NAG 2 n C NAG 2 C 2 NAG C 3 NAG 2 n C FUC 3 C 3 FUC D 1 FUC 3 n D NAG 1 D 1 NAG C 5 NAG 3 n D NAG 2 D 2 NAG C 6 NAG 2 n E NAG 1 E 1 NAG C 2 NAG 2 n E NAG 2 E 2 NAG C 4 NAG 2 n E FUC 3 E 3 FUC D 2 FUC # 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 20 A CYS 31 1_555 A SG CYS 329 A CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf2 A SG CYS 377 A CYS 388 1_555 A SG CYS 381 A CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf3 B SG CYS 20 B CYS 31 1_555 B SG CYS 329 B CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 B SG CYS 377 B CYS 388 1_555 B SG CYS 381 B CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A ND2 ASN 162 A ASN 173 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 A ND2 ASN 248 A ASN 259 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale3 B ND2 ASN 162 B ASN 173 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _chem_comp.formula 'I -1' _chem_comp.formula_weight 126.904 _chem_comp.id IOD _chem_comp.mon_nstd_flag . _chem_comp.name 'IODIDE ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5U84 _atom_sites.fract_transf_matrix[1][1] 0.008416 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001939 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009152 _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] 0.012901 _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 F 4 I3C A 1 406 2 I3C I3C . G 4 I3C A 1 407 3 I3C I3C . H 4 I3C A 1 408 4 I3C I3C . I 4 I3C A 1 409 5 I3C I3C . J 4 I3C A 1 410 6 I3C I3C . K 4 I3C A 1 411 8 I3C I3C . L 4 I3C A 1 412 9 I3C I3C . M 5 IOD A 1 413 1 IOD IOD . N 5 IOD A 1 414 2 IOD IOD . O 5 IOD A 1 415 3 IOD IOD . P 5 IOD A 1 416 5 IOD IOD . Q 5 IOD A 1 417 6 IOD IOD . R 5 IOD A 1 418 8 IOD IOD . S 5 IOD A 1 419 9 IOD IOD . T 5 IOD A 1 420 14 IOD IOD . U 5 IOD A 1 421 16 IOD IOD . V 5 IOD A 1 422 19 IOD IOD . W 5 IOD A 1 423 20 IOD IOD . X 5 IOD A 1 424 22 IOD IOD . Y 5 IOD A 1 425 24 IOD IOD . Z 5 IOD A 1 426 26 IOD IOD . AA 5 IOD A 1 427 28 IOD IOD . BA 5 IOD A 1 428 29 IOD IOD . CA 5 IOD A 1 429 30 IOD IOD . DA 5 IOD A 1 430 34 IOD IOD . EA 4 I3C B 1 404 1 I3C I3C . FA 4 I3C B 1 405 7 I3C I3C . GA 5 IOD B 1 406 4 IOD IOD . HA 5 IOD B 1 407 7 IOD IOD . IA 5 IOD B 1 408 10 IOD IOD . JA 5 IOD B 1 409 11 IOD IOD . KA 5 IOD B 1 410 12 IOD IOD . LA 5 IOD B 1 411 13 IOD IOD . MA 5 IOD B 1 412 15 IOD IOD . NA 5 IOD B 1 413 17 IOD IOD . OA 5 IOD B 1 414 18 IOD IOD . PA 5 IOD B 1 415 21 IOD IOD . QA 5 IOD B 1 416 23 IOD IOD . RA 5 IOD B 1 417 25 IOD IOD . SA 5 IOD B 1 418 27 IOD IOD . TA 5 IOD B 1 419 31 IOD IOD . UA 5 IOD B 1 420 32 IOD IOD . VA 5 IOD B 1 421 33 IOD IOD . WA 6 HOH A 1 501 53 HOH HOH . WA 6 HOH A 2 502 61 HOH HOH . WA 6 HOH A 3 503 22 HOH HOH . WA 6 HOH A 4 504 76 HOH HOH . WA 6 HOH A 5 505 36 HOH HOH . WA 6 HOH A 6 506 80 HOH HOH . WA 6 HOH A 7 507 73 HOH HOH . WA 6 HOH A 8 508 72 HOH HOH . WA 6 HOH A 9 509 60 HOH HOH . WA 6 HOH A 10 510 17 HOH HOH . WA 6 HOH A 11 511 68 HOH HOH . WA 6 HOH A 12 512 23 HOH HOH . WA 6 HOH A 13 513 62 HOH HOH . WA 6 HOH A 14 514 81 HOH HOH . WA 6 HOH A 15 515 34 HOH HOH . WA 6 HOH A 16 516 59 HOH HOH . WA 6 HOH A 17 517 75 HOH HOH . WA 6 HOH A 18 518 6 HOH HOH . WA 6 HOH A 19 519 35 HOH HOH . WA 6 HOH A 20 520 30 HOH HOH . WA 6 HOH A 21 521 102 HOH HOH . WA 6 HOH A 22 522 66 HOH HOH . WA 6 HOH A 23 523 7 HOH HOH . WA 6 HOH A 24 524 91 HOH HOH . WA 6 HOH A 25 525 10 HOH HOH . WA 6 HOH A 26 526 1 HOH HOH . WA 6 HOH A 27 527 8 HOH HOH . WA 6 HOH A 28 528 98 HOH HOH . WA 6 HOH A 29 529 67 HOH HOH . WA 6 HOH A 30 530 27 HOH HOH . WA 6 HOH A 31 531 117 HOH HOH . WA 6 HOH A 32 532 125 HOH HOH . WA 6 HOH A 33 533 96 HOH HOH . WA 6 HOH A 34 534 38 HOH HOH . WA 6 HOH A 35 535 121 HOH HOH . WA 6 HOH A 36 536 65 HOH HOH . WA 6 HOH A 37 537 111 HOH HOH . WA 6 HOH A 38 538 109 HOH HOH . WA 6 HOH A 39 539 20 HOH HOH . WA 6 HOH A 40 540 114 HOH HOH . WA 6 HOH A 41 541 133 HOH HOH . WA 6 HOH A 42 542 33 HOH HOH . WA 6 HOH A 43 543 77 HOH HOH . WA 6 HOH A 44 544 69 HOH HOH . WA 6 HOH A 45 545 47 HOH HOH . WA 6 HOH A 46 546 54 HOH HOH . WA 6 HOH A 47 547 127 HOH HOH . WA 6 HOH A 48 548 18 HOH HOH . WA 6 HOH A 49 549 26 HOH HOH . WA 6 HOH A 50 550 122 HOH HOH . WA 6 HOH A 51 551 2 HOH HOH . WA 6 HOH A 52 552 12 HOH HOH . WA 6 HOH A 53 553 11 HOH HOH . WA 6 HOH A 54 554 48 HOH HOH . WA 6 HOH A 55 555 19 HOH HOH . WA 6 HOH A 56 556 123 HOH HOH . WA 6 HOH A 57 557 51 HOH HOH . WA 6 HOH A 58 558 64 HOH HOH . WA 6 HOH A 59 559 71 HOH HOH . WA 6 HOH A 60 560 86 HOH HOH . WA 6 HOH A 61 561 49 HOH HOH . WA 6 HOH A 62 562 45 HOH HOH . WA 6 HOH A 63 563 101 HOH HOH . WA 6 HOH A 64 564 83 HOH HOH . WA 6 HOH A 65 565 55 HOH HOH . WA 6 HOH A 66 566 134 HOH HOH . WA 6 HOH A 67 567 13 HOH HOH . WA 6 HOH A 68 568 46 HOH HOH . WA 6 HOH A 69 569 43 HOH HOH . WA 6 HOH A 70 570 63 HOH HOH . WA 6 HOH A 71 571 3 HOH HOH . WA 6 HOH A 72 572 130 HOH HOH . WA 6 HOH A 73 573 39 HOH HOH . WA 6 HOH A 74 574 88 HOH HOH . WA 6 HOH A 75 575 57 HOH HOH . WA 6 HOH A 76 576 105 HOH HOH . WA 6 HOH A 77 577 70 HOH HOH . WA 6 HOH A 78 578 14 HOH HOH . WA 6 HOH A 79 579 82 HOH HOH . WA 6 HOH A 80 580 120 HOH HOH . WA 6 HOH A 81 581 40 HOH HOH . WA 6 HOH A 82 582 78 HOH HOH . WA 6 HOH A 83 583 93 HOH HOH . WA 6 HOH A 84 584 129 HOH HOH . WA 6 HOH A 85 585 92 HOH HOH . WA 6 HOH A 86 586 112 HOH HOH . WA 6 HOH A 87 587 97 HOH HOH . WA 6 HOH A 88 588 24 HOH HOH . WA 6 HOH A 89 589 74 HOH HOH . WA 6 HOH A 90 590 37 HOH HOH . WA 6 HOH A 91 591 115 HOH HOH . WA 6 HOH A 92 592 50 HOH HOH . WA 6 HOH A 93 593 132 HOH HOH . XA 6 HOH B 1 501 100 HOH HOH . XA 6 HOH B 2 502 87 HOH HOH . XA 6 HOH B 3 503 56 HOH HOH . XA 6 HOH B 4 504 106 HOH HOH . XA 6 HOH B 5 505 25 HOH HOH . XA 6 HOH B 6 506 31 HOH HOH . XA 6 HOH B 7 507 108 HOH HOH . XA 6 HOH B 8 508 85 HOH HOH . XA 6 HOH B 9 509 42 HOH HOH . XA 6 HOH B 10 510 79 HOH HOH . XA 6 HOH B 11 511 44 HOH HOH . XA 6 HOH B 12 512 128 HOH HOH . XA 6 HOH B 13 513 9 HOH HOH . XA 6 HOH B 14 514 103 HOH HOH . XA 6 HOH B 15 515 99 HOH HOH . XA 6 HOH B 16 516 4 HOH HOH . XA 6 HOH B 17 517 107 HOH HOH . XA 6 HOH B 18 518 113 HOH HOH . XA 6 HOH B 19 519 90 HOH HOH . XA 6 HOH B 20 520 5 HOH HOH . XA 6 HOH B 21 521 104 HOH HOH . XA 6 HOH B 22 522 16 HOH HOH . XA 6 HOH B 23 523 118 HOH HOH . XA 6 HOH B 24 524 29 HOH HOH . XA 6 HOH B 25 525 41 HOH HOH . XA 6 HOH B 26 526 28 HOH HOH . XA 6 HOH B 27 527 52 HOH HOH . XA 6 HOH B 28 528 21 HOH HOH . XA 6 HOH B 29 529 15 HOH HOH . XA 6 HOH B 30 530 94 HOH HOH . XA 6 HOH B 31 531 89 HOH HOH . XA 6 HOH B 32 532 110 HOH HOH . XA 6 HOH B 33 533 58 HOH HOH . XA 6 HOH B 34 534 124 HOH HOH . XA 6 HOH B 35 535 84 HOH HOH . XA 6 HOH B 36 536 116 HOH HOH . XA 6 HOH B 37 537 95 HOH HOH . XA 6 HOH B 38 538 32 HOH HOH . XA 6 HOH B 39 539 126 HOH HOH . XA 6 HOH B 40 540 119 HOH HOH . XA 6 HOH B 41 541 131 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol I _atom_site.label_atom_id I _atom_site.label_comp_id IOD _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id Z _atom_site.label_entity_id 5 _atom_site.Cartn_x 13.454 _atom_site.Cartn_y -39.487 _atom_site.Cartn_z 24.558 _atom_site.occupancy 0.35 _atom_site.B_iso_or_equiv 68.51 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id I _atom_site.auth_comp_id IOD _atom_site.auth_seq_id 426 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 1 #