data_4CVM # _model_server_result.job_id v5bCa-dJX4wB6IGPBMfBZA _model_server_result.datetime_utc '2024-11-05 00:18:20' _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 4cvm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1452}' # _entry.id 4CVM # _exptl.entry_id 4CVM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _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 4CVM _cell.length_a 58.54 _cell.length_b 86.05 _cell.length_c 88.24 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CVM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 3 _struct_asym.id C _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 covale ? covale1 C PB UDP . A UDP 1452 1_555 D O1 MUB . A MUB 1453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.688 ? covale ? covale2 D C10 MUB . A MUB 1453 1_555 B N ALA . A ALA 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B C ALA . A ALA 1454 1_555 E N FGA . A FGA 1455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.368 ? metalc ? metalc1 A OG1 THR 114 A THR 114 1_555 G MG MG . A MG 1457 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc2 A OG1 THR 114 A THR 114 1_555 H MG MG . A MG 1458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc3 A OD1 ASN 140 A ASN 140 1_555 G MG MG . A MG 1457 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc4 A OD1 ASN 140 A ASN 140 1_555 H MG MG . A MG 1458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.89 ? metalc ? metalc5 A OE2 GLU 164 A GLU 164 1_555 H MG MG . A MG 1458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc6 F O2A ANP . A ANP 1456 1_555 G MG MG . A MG 1457 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.761 ? metalc ? metalc7 F O2B ANP . A ANP 1456 1_555 G MG MG . A MG 1457 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc8 F O2G ANP . A ANP 1456 1_555 H MG MG . A MG 1458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc9 F O2B ANP . A ANP 1456 1_555 H MG MG . A MG 1458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? # _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 465 n n N1 C6 UDP sing 466 n n N1 C1' UDP sing 467 n n C2 N3 UDP sing 468 n n C2 O2 UDP doub 469 n n N3 C4 UDP sing 470 n n N3 HN3 UDP sing 471 n n C4 C5 UDP sing 472 n n C4 O4 UDP doub 473 n n C5 C6 UDP doub 474 n n C5 H5 UDP sing 475 n n C6 H6 UDP sing 476 n n C1' C2' UDP sing 477 n n C1' O4' UDP sing 478 n n C1' H1' UDP sing 479 n n C2' O2' UDP sing 480 n n C2' C3' UDP sing 481 n n C2' H2' UDP sing 482 n n O2' HO2' UDP sing 483 n n C3' C4' UDP sing 484 n n C3' O3' UDP sing 485 n n C3' H3' UDP sing 486 n n C4' O4' UDP sing 487 n n C4' C5' UDP sing 488 n n C4' H4' UDP sing 489 n n O3' HO3' UDP sing 490 n n C5' O5' UDP sing 491 n n C5' "H5'1" UDP sing 492 n n C5' "H5'2" UDP sing 493 n n O5' PA UDP sing 494 n n PA O1A UDP doub 495 n n PA O2A UDP sing 496 n n PA O3A UDP sing 497 n n O2A HOA2 UDP sing 498 n n O3A PB UDP sing 499 n n PB O1B UDP doub 500 n n PB O2B UDP sing 501 n n PB O3B UDP sing 502 n n O2B HOB2 UDP sing 503 n n O3B HOB3 UDP sing 504 n n # _atom_sites.entry_id 4CVM _atom_sites.fract_transf_matrix[1][1] 0.017082 _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] 0.011621 _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] 0.011333 _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 B 2 ALA A 1 1454 1454 ALA ALA . C 3 UDP A 1 1452 1452 UDP UDP . D 4 MUB A 1 1453 1453 MUB MUB . E 5 FGA A 1 1455 1455 FGA FGA . F 6 ANP A 1 1456 1456 ANP ANP . G 7 MG A 1 1457 1457 MG MG . H 7 MG A 1 1458 1458 MG MG . I 8 HOH A 1 2001 2001 HOH HOH . I 8 HOH A 2 2002 2002 HOH HOH . I 8 HOH A 3 2003 2003 HOH HOH . I 8 HOH A 4 2004 2004 HOH HOH . I 8 HOH A 5 2005 2005 HOH HOH . I 8 HOH A 6 2006 2006 HOH HOH . I 8 HOH A 7 2007 2007 HOH HOH . I 8 HOH A 8 2008 2008 HOH HOH . I 8 HOH A 9 2009 2009 HOH HOH . I 8 HOH A 10 2010 2010 HOH HOH . I 8 HOH A 11 2011 2011 HOH HOH . I 8 HOH A 12 2012 2012 HOH HOH . I 8 HOH A 13 2013 2013 HOH HOH . I 8 HOH A 14 2014 2014 HOH HOH . I 8 HOH A 15 2015 2015 HOH HOH . I 8 HOH A 16 2016 2016 HOH HOH . I 8 HOH A 17 2017 2017 HOH HOH . I 8 HOH A 18 2018 2018 HOH HOH . I 8 HOH A 19 2019 2019 HOH HOH . I 8 HOH A 20 2020 2020 HOH HOH . I 8 HOH A 21 2021 2021 HOH HOH . I 8 HOH A 22 2022 2022 HOH HOH . I 8 HOH A 23 2023 2023 HOH HOH . I 8 HOH A 24 2024 2024 HOH HOH . I 8 HOH A 25 2025 2025 HOH HOH . I 8 HOH A 26 2026 2026 HOH HOH . I 8 HOH A 27 2027 2027 HOH HOH . I 8 HOH A 28 2028 2028 HOH HOH . I 8 HOH A 29 2029 2029 HOH HOH . I 8 HOH A 30 2030 2030 HOH HOH . I 8 HOH A 31 2031 2031 HOH HOH . I 8 HOH A 32 2032 2032 HOH HOH . I 8 HOH A 33 2033 2033 HOH HOH . I 8 HOH A 34 2034 2034 HOH HOH . I 8 HOH A 35 2035 2035 HOH HOH . I 8 HOH A 36 2036 2036 HOH HOH . I 8 HOH A 37 2037 2037 HOH HOH . I 8 HOH A 38 2038 2038 HOH HOH . I 8 HOH A 39 2039 2039 HOH HOH . I 8 HOH A 40 2040 2040 HOH HOH . I 8 HOH A 41 2041 2041 HOH HOH . I 8 HOH A 42 2042 2042 HOH HOH . I 8 HOH A 43 2043 2043 HOH HOH . I 8 HOH A 44 2044 2044 HOH HOH . I 8 HOH A 45 2045 2045 HOH HOH . I 8 HOH A 46 2046 2046 HOH HOH . I 8 HOH A 47 2047 2047 HOH HOH . I 8 HOH A 48 2048 2048 HOH HOH . I 8 HOH A 49 2049 2049 HOH HOH . I 8 HOH A 50 2050 2050 HOH HOH . I 8 HOH A 51 2051 2051 HOH HOH . I 8 HOH A 52 2052 2052 HOH HOH . I 8 HOH A 53 2053 2053 HOH HOH . I 8 HOH A 54 2054 2054 HOH HOH . I 8 HOH A 55 2055 2055 HOH HOH . I 8 HOH A 56 2056 2056 HOH HOH . I 8 HOH A 57 2057 2057 HOH HOH . I 8 HOH A 58 2058 2058 HOH HOH . I 8 HOH A 59 2059 2059 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 . . . C 3 10.929 -25.891 -36.085 1 28.66 ? N1 UDP 1452 A 1 HETATM 2 C C2 UDP . . . C 3 9.893 -26.5 -36.735 1 25.36 ? C2 UDP 1452 A 1 HETATM 3 N N3 UDP . . . C 3 10.145 -27.436 -37.684 1 24.7 ? N3 UDP 1452 A 1 HETATM 4 C C4 UDP . . . C 3 11.46 -27.775 -38.033 1 29.12 ? C4 UDP 1452 A 1 HETATM 5 C C5 UDP . . . C 3 12.519 -27.154 -37.399 1 29.36 ? C5 UDP 1452 A 1 HETATM 6 C C6 UDP . . . C 3 12.247 -26.224 -36.4 1 28.3 ? C6 UDP 1452 A 1 HETATM 7 O O2 UDP . . . C 3 8.726 -26.245 -36.491 1 22.14 ? O2 UDP 1452 A 1 HETATM 8 O O4 UDP . . . C 3 11.654 -28.638 -38.895 1 33.18 ? O4 UDP 1452 A 1 HETATM 9 C C1' UDP . . . C 3 10.703 -24.882 -35.036 1 26.99 ? C1' UDP 1452 A 1 HETATM 10 C C2' UDP . . . C 3 11.264 -25.371 -33.718 1 25.37 ? C2' UDP 1452 A 1 HETATM 11 O O2' UDP . . . C 3 10.407 -26.303 -33.052 1 23.88 ? O2' UDP 1452 A 1 HETATM 12 C C3' UDP . . . C 3 11.387 -24.091 -32.984 1 24.8 ? C3' UDP 1452 A 1 HETATM 13 C C4' UDP . . . C 3 11.644 -23.065 -34.145 1 27.9 ? C4' UDP 1452 A 1 HETATM 14 O O4' UDP . . . C 3 11.598 -23.81 -35.328 1 27.73 ? O4' UDP 1452 A 1 HETATM 15 O O3' UDP . . . C 3 10.195 -23.724 -32.324 1 22.79 ? O3' UDP 1452 A 1 HETATM 16 C C5' UDP . . . C 3 13.063 -22.469 -33.995 1 29.12 ? C5' UDP 1452 A 1 HETATM 17 O O5' UDP . . . C 3 13.934 -23.568 -33.98 1 30.27 ? O5' UDP 1452 A 1 HETATM 18 P PA UDP . . . C 3 15.353 -23.36 -33.286 1 32.21 ? PA UDP 1452 A 1 HETATM 19 O O1A UDP . . . C 3 16.037 -22.276 -34.156 1 27.18 ? O1A UDP 1452 A 1 HETATM 20 O O2A UDP . . . C 3 15.206 -22.781 -31.892 1 31.56 ? O2A UDP 1452 A 1 HETATM 21 O O3A UDP . . . C 3 16.192 -24.652 -33.391 1 32.23 ? O3A UDP 1452 A 1 HETATM 22 P PB UDP . . . C 3 15.839 -26.184 -33.019 1 33.28 ? PB UDP 1452 A 1 HETATM 23 O O1B UDP . . . C 3 14.59 -26.725 -33.753 1 34.15 ? O1B UDP 1452 A 1 HETATM 24 O O3B UDP . . . C 3 16.937 -27.083 -33.13 1 32.88 ? O3B UDP 1452 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #