data_2VBT # _model_server_result.job_id KPlBwn5La_4SYDQFzAMlJg _model_server_result.datetime_utc '2024-11-28 06:06:40' _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 2vbt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1137}' # _entry.id 2VBT # _exptl.entry_id 2VBT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.176 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-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 2VBT _cell.length_a 77.72 _cell.length_b 77.72 _cell.length_c 106.868 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VBT _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 PQS _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 _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 2 _struct_asym.id B _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 A OG1 THR 43 A THR 43 1_555 C NA NA . A NA 1138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc2 B O2B CDP . A CDP 1137 1_555 C NA NA . A NA 1138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? # _chem_comp.formula 'C9 H15 N3 O11 P2' _chem_comp.formula_weight 403.176 _chem_comp.id CDP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-DIPHOSPHATE" _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 O3B PB CDP sing 70 n n PB O1B CDP doub 71 n n PB O2B CDP sing 72 n n PB O3A CDP sing 73 n n O3A PA CDP sing 74 n n PA O1A CDP doub 75 n n PA O2A CDP sing 76 n n PA O5' CDP sing 77 n n O5' C5' CDP sing 78 n n C5' C4' CDP sing 79 n n C5' "H5'1" CDP sing 80 n n C5' "H5'2" CDP sing 81 n n C4' O4' CDP sing 82 n n C4' C3' CDP sing 83 n n C4' H4' CDP sing 84 n n O4' C1' CDP sing 85 n n C3' O3' CDP sing 86 n n C3' C2' CDP sing 87 n n C3' H3' CDP sing 88 n n O3' HA CDP sing 89 n n C2' O2' CDP sing 90 n n C2' C1' CDP sing 91 n n C2' H2' CDP sing 92 n n O2' HB CDP sing 93 n n C1' N1 CDP sing 94 n n C1' H1' CDP sing 95 n n N1 C2 CDP sing 96 n n N1 C6 CDP sing 97 n n C2 O2 CDP doub 98 n n C2 N3 CDP sing 99 n n N3 C4 CDP doub 100 n n C4 N4 CDP sing 101 n n C4 C5 CDP sing 102 n n N4 H4N1 CDP sing 103 n n N4 H4N2 CDP sing 104 n n C5 C6 CDP doub 105 n n C5 H5 CDP sing 106 n n C6 H6 CDP sing 107 n n HO1 O2A CDP sing 108 n n HO2 O2B CDP sing 109 n n HO3 O3B CDP sing 110 n n # _atom_sites.entry_id 2VBT _atom_sites.fract_transf_matrix[1][1] 0.012867 _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] 0.012867 _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] 0.009357 _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 CDP A 1 1137 1137 CDP CDP . C 3 NA A 1 1138 1138 NA NA . D 4 PO4 A 1 1139 1139 PO4 PO4 . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . E 5 HOH A 23 2023 2023 HOH HOH . E 5 HOH A 24 2024 2024 HOH HOH . E 5 HOH A 25 2025 2025 HOH HOH . E 5 HOH A 26 2026 2026 HOH HOH . E 5 HOH A 27 2027 2027 HOH HOH . E 5 HOH A 28 2028 2028 HOH HOH . E 5 HOH A 29 2029 2029 HOH HOH . E 5 HOH A 30 2030 2030 HOH HOH . E 5 HOH A 31 2031 2031 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 O O3B CDP . . . B 2 -33.254 8.411 -4.602 1 75.33 ? O3B CDP 1137 A 1 HETATM 2 P PB CDP . . . B 2 -33.023 7.036 -4.172 1 74.69 ? PB CDP 1137 A 1 HETATM 3 O O1B CDP . . . B 2 -32.114 6.342 -5.085 1 73.38 ? O1B CDP 1137 A 1 HETATM 4 O O2B CDP . . . B 2 -34.197 6.276 -3.715 1 75.62 ? O2B CDP 1137 A 1 HETATM 5 O O3A CDP . . . B 2 -32.216 7.167 -2.81 1 76.36 ? O3A CDP 1137 A 1 HETATM 6 P PA CDP . . . B 2 -32.58 8.062 -1.536 1 74.03 ? PA CDP 1137 A 1 HETATM 7 O O1A CDP . . . B 2 -33.049 7.171 -0.471 1 73.39 ? O1A CDP 1137 A 1 HETATM 8 O O2A CDP . . . B 2 -33.389 9.227 -1.884 1 75.12 ? O2A CDP 1137 A 1 HETATM 9 O O5' CDP . . . B 2 -31.205 8.668 -1.115 1 73.15 ? O5' CDP 1137 A 1 HETATM 10 C C5' CDP . . . B 2 -30.974 10.033 -1.342 1 71.63 ? C5' CDP 1137 A 1 HETATM 11 C C4' CDP . . . B 2 -29.946 10.197 -2.435 1 69.96 ? C4' CDP 1137 A 1 HETATM 12 O O4' CDP . . . B 2 -28.668 10.028 -1.882 1 69.15 ? O4' CDP 1137 A 1 HETATM 13 C C3' CDP . . . B 2 -30.09 9.118 -3.462 1 68.81 ? C3' CDP 1137 A 1 HETATM 14 O O3' CDP . . . B 2 -29.818 9.719 -4.713 1 68.98 ? O3' CDP 1137 A 1 HETATM 15 C C2' CDP . . . B 2 -28.966 8.168 -3.202 1 67.97 ? C2' CDP 1137 A 1 HETATM 16 O O2' CDP . . . B 2 -28.527 7.699 -4.462 1 64.5 ? O2' CDP 1137 A 1 HETATM 17 C C1' CDP . . . B 2 -27.926 9.061 -2.586 1 68.16 ? C1' CDP 1137 A 1 HETATM 18 N N1 CDP . . . B 2 -27.199 8.359 -1.563 1 67.65 ? N1 CDP 1137 A 1 HETATM 19 C C2 CDP . . . B 2 -25.827 8.259 -1.572 1 66.86 ? C2 CDP 1137 A 1 HETATM 20 O O2 CDP . . . B 2 -25.187 8.769 -2.476 1 67.54 ? O2 CDP 1137 A 1 HETATM 21 N N3 CDP . . . B 2 -25.185 7.618 -0.612 1 67.33 ? N3 CDP 1137 A 1 HETATM 22 C C4 CDP . . . B 2 -25.872 7.075 0.377 1 66.68 ? C4 CDP 1137 A 1 HETATM 23 N N4 CDP . . . B 2 -25.247 6.428 1.354 1 67.24 ? N4 CDP 1137 A 1 HETATM 24 C C5 CDP . . . B 2 -27.223 7.165 0.41 1 67.1 ? C5 CDP 1137 A 1 HETATM 25 C C6 CDP . . . B 2 -27.882 7.828 -0.586 1 67.97 ? C6 CDP 1137 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #