data_6HIZ # _model_server_result.job_id KKJPicQb4-vcpDJEmv4mcQ _model_server_result.datetime_utc '2024-11-22 01:49:33' _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 6hiz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","auth_seq_id":401}' # _entry.id 6HIZ # _exptl.entry_id 6HIZ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 484.141 _entity.id 30 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _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 6HIZ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6HIZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 28-meric _pdbx_struct_assembly.oligomeric_count 28 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA _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 ? _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 30 _struct_asym.id DA _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # 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 metalc ? metalc1 W OG SER 156 Cg SER 156 1_555 FA MG MG . Cg MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc2 EA O3G GTP . Cg GTP 501 1_555 FA MG MG . Cg MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc3 EA O2B GTP . Cg GTP 501 1_555 FA MG MG . Cg MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc4 FA MG MG . Cg MG 502 1_555 JA O HOH . Cg HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc5 FA MG MG . Cg MG 502 1_555 JA O HOH . Cg HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc6 FA MG MG . Cg MG 502 1_555 JA O HOH . Cg HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? hydrog 'U-A PAIR' hydrog1 Z O2 U 398 CA U 398 1_555 Z N6 A 534 CA A 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 Z N3 U 402 CA U 402 1_555 Z N1 A 526 CA A 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 Z O4 U 402 CA U 402 1_555 Z N6 A 526 CA A 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 Z N3 U 403 CA U 403 1_555 Z N1 A 525 CA A 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 Z O4 U 403 CA U 403 1_555 Z N6 A 525 CA A 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 Z N3 U 404 CA U 404 1_555 Z N1 A 524 CA A 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 Z O4 U 404 CA U 404 1_555 Z N6 A 524 CA A 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 Z N1 A 405 CA A 405 1_555 Z N3 U 523 CA U 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 Z N6 A 405 CA A 405 1_555 Z O4 U 523 CA U 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 Z N3 U 406 CA U 406 1_555 Z N1 A 522 CA A 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 Z O4 U 406 CA U 406 1_555 Z N6 A 522 CA A 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-U MISPAIR' hydrog12 Z O2 U 440 CA U 440 1_555 Z N3 U 479 CA U 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog13 Z N2 G 441 CA G 441 1_555 Z N3 A 447 CA A 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-C MISPAIR' hydrog14 Z O4 U 443 CA U 443 1_555 Z N4 C 446 CA C 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-A MISPAIR' hydrog15 Z N4 C 446 CA C 446 1_555 Z N3 A 478 CA A 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-U MISPAIR' hydrog16 Z O4 U 451 CA U 451 1_555 Z N3 U 474 CA U 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-U MISPAIR' hydrog17 Z N2 G 455 CA G 455 1_555 Z O2 U 465 CA U 465 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H15 N2 O15 P3' _chem_comp.formula_weight 484.141 _chem_comp.id UTP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE 5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 PA O1A UTP doub 586 n n PA O2A UTP sing 587 n n PA O3A UTP sing 588 n n PA O5' UTP sing 589 n n O2A H2A UTP sing 590 n n O3A PB UTP sing 591 n n O5' C5' UTP sing 592 n n PB O1B UTP sing 593 n n PB O2B UTP doub 594 n n PB O3B UTP sing 595 n n O1B H1B UTP sing 596 n n O3B PG UTP sing 597 n n PG O1G UTP sing 598 n n PG O2G UTP doub 599 n n PG O3G UTP sing 600 n n O1G H1G UTP sing 601 n n O3G H3G UTP sing 602 n n C5' C4' UTP sing 603 n n C5' "H5'1" UTP sing 604 n n C5' "H5'2" UTP sing 605 n n C4' O4' UTP sing 606 n n C4' C3' UTP sing 607 n n C4' H4' UTP sing 608 n n O4' C1' UTP sing 609 n n C1' C2' UTP sing 610 n n C1' N1 UTP sing 611 n n C1' H1' UTP sing 612 n n C2' O2' UTP sing 613 n n C2' C3' UTP sing 614 n n C2' H2' UTP sing 615 n n O2' HA UTP sing 616 n n C3' O3' UTP sing 617 n n C3' H3' UTP sing 618 n n O3' HB UTP sing 619 n n N1 C6 UTP sing 620 n y N1 C2 UTP sing 621 n y C6 C5 UTP doub 622 n y C6 H6 UTP sing 623 n n C2 O2 UTP doub 624 n n C2 N3 UTP sing 625 n y N3 C4 UTP sing 626 n y N3 H3 UTP sing 627 n n C4 O4 UTP doub 628 n n C4 C5 UTP sing 629 n y C5 H5 UTP sing 630 n n # _atom_sites.entry_id 6HIZ _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 CA 29 SPD DL 1 401 101 SPD SPD . DA 30 UTP DJ 1 401 200 UTP UTP . EA 31 GTP Cg 1 501 501 GTP GTP . FA 32 MG Cg 1 502 502 MG MG . GA 32 MG CA 1 701 1 MG MG . HA 32 MG CA 1 702 2 MG MG . IA 29 SPD CA 1 703 100 SPD SPD . JA 33 HOH Cg 1 601 503 HOH HOH . JA 33 HOH Cg 2 602 504 HOH HOH . JA 33 HOH Cg 3 603 505 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 P PA UTP . . . DA 30 299.748 275.833 198.624 1 79.65 0 PA UTP 401 DJ 1 HETATM 2 O O1A UTP . . . DA 30 298.274 275.876 198.303 1 100.73 -1 O1A UTP 401 DJ 1 HETATM 3 O O2A UTP . . . DA 30 300.287 276.723 199.679 1 62.99 0 O2A UTP 401 DJ 1 HETATM 4 O O3A UTP . . . DA 30 300.627 276.164 197.308 1 73.94 0 O3A UTP 401 DJ 1 HETATM 5 O O5' UTP . . . DA 30 300.167 274.232 198.88 1 62.88 0 O5' UTP 401 DJ 1 HETATM 6 P PB UTP . . . DA 30 300.277 277.19 196.067 1 75.95 0 PB UTP 401 DJ 1 HETATM 7 O O1B UTP . . . DA 30 299.133 278.114 196.336 1 66.16 0 O1B UTP 401 DJ 1 HETATM 8 O O2B UTP . . . DA 30 301.6 277.746 195.635 1 144.84 -1 O2B UTP 401 DJ 1 HETATM 9 O O3B UTP . . . DA 30 299.865 276.083 194.967 1 79.27 0 O3B UTP 401 DJ 1 HETATM 10 P PG UTP . . . DA 30 298.894 276.327 193.712 1 91.19 0 PG UTP 401 DJ 1 HETATM 11 O O1G UTP . . . DA 30 299.017 277.762 193.439 1 122.64 -1 O1G UTP 401 DJ 1 HETATM 12 O O2G UTP . . . DA 30 299.553 275.454 192.713 1 64.61 0 O2G UTP 401 DJ 1 HETATM 13 O O3G UTP . . . DA 30 297.571 275.898 194.152 1 69.13 0 O3G UTP 401 DJ 1 HETATM 14 C C5' UTP . . . DA 30 301.325 273.586 198.263 1 54.4 0 C5' UTP 401 DJ 1 HETATM 15 C C4' UTP . . . DA 30 300.849 272.457 197.342 1 46.56 0 C4' UTP 401 DJ 1 HETATM 16 O O4' UTP . . . DA 30 299.523 272.206 197.724 1 49.71 0 O4' UTP 401 DJ 1 HETATM 17 C C1' UTP . . . DA 30 298.924 271.509 196.592 1 69.08 0 C1' UTP 401 DJ 1 HETATM 18 C C2' UTP . . . DA 30 299.668 272.044 195.317 1 58.12 0 C2' UTP 401 DJ 1 HETATM 19 O O2' UTP . . . DA 30 300.428 270.98 194.748 1 57.54 0 O2' UTP 401 DJ 1 HETATM 20 C C3' UTP . . . DA 30 300.627 273.026 195.961 1 59.04 0 C3' UTP 401 DJ 1 HETATM 21 O O3' UTP . . . DA 30 301.883 273.115 195.242 1 53.41 0 O3' UTP 401 DJ 1 HETATM 22 N N1 UTP . . . DA 30 297.399 271.597 196.708 1 66.98 0 N1 UTP 401 DJ 1 HETATM 23 C C6 UTP . . . DA 30 296.736 270.486 197.254 1 53.4 0 C6 UTP 401 DJ 1 HETATM 24 C C2 UTP . . . DA 30 296.656 272.681 196.372 1 54.11 0 C2 UTP 401 DJ 1 HETATM 25 O O2 UTP . . . DA 30 297.18 273.69 195.897 1 51.31 0 O2 UTP 401 DJ 1 HETATM 26 N N3 UTP . . . DA 30 295.262 272.666 196.544 1 49.72 0 N3 UTP 401 DJ 1 HETATM 27 C C4 UTP . . . DA 30 294.611 271.556 197.068 1 53.67 0 C4 UTP 401 DJ 1 HETATM 28 O O4 UTP . . . DA 30 293.39 271.543 197.21 1 49.79 0 O4 UTP 401 DJ 1 HETATM 29 C C5 UTP . . . DA 30 295.352 270.433 197.436 1 45.13 0 C5 UTP 401 DJ 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 180 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 29 #