data_2V4Z # _model_server_result.job_id RjpOwPe2z29mUyK5iGTB4Q _model_server_result.datetime_utc '2024-11-08 16:58:00' _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 2v4z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1348}' # _entry.id 2V4Z # _exptl.entry_id 2V4Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-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 120 _cell.entry_id 2V4Z _cell.length_a 114.539 _cell.length_b 114.539 _cell.length_c 99.33 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2V4Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PQS _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 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 metalc ? metalc1 A OG SER 46 A SER 47 1_555 E MG MG . A MG 1350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc2 A OG1 THR 180 A THR 181 1_555 E MG MG . A MG 1350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? metalc ? metalc3 C O2B GDP . A GDP 1348 1_555 D AL ALF . A ALF 1349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.776 ? metalc ? metalc4 C O3B GDP . A GDP 1348 1_555 E MG MG . A MG 1350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? metalc ? metalc5 D F2 ALF . A ALF 1349 1_555 E MG MG . A MG 1350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.782 ? metalc ? metalc6 D AL ALF . A ALF 1349 1_555 E MG MG . A MG 1350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.107 ? metalc ? metalc7 D F4 ALF . A ALF 1349 1_555 E MG MG . A MG 1350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc8 D AL ALF . A ALF 1349 1_555 F O HOH . A HOH 2012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc9 E MG MG . A MG 1350 1_555 F O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc10 E MG MG . A MG 1350 1_555 F O HOH . A HOH 2015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-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 PB O1B GDP doub 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 2V4Z _atom_sites.fract_transf_matrix[1][1] 0.008731 _atom_sites.fract_transf_matrix[1][2] 0.005041 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010081 _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] 0.010067 _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 C 3 GDP A 1 1348 1348 GDP GDP . D 4 ALF A 1 1349 1349 ALF ALF . E 5 MG A 1 1350 1350 MG MG . F 6 HOH A 1 2001 2001 HOH HOH . F 6 HOH A 2 2002 2002 HOH HOH . F 6 HOH A 3 2003 2003 HOH HOH . F 6 HOH A 4 2004 2004 HOH HOH . F 6 HOH A 5 2005 2005 HOH HOH . F 6 HOH A 6 2006 2006 HOH HOH . F 6 HOH A 7 2007 2007 HOH HOH . F 6 HOH A 8 2008 2008 HOH HOH . F 6 HOH A 9 2009 2009 HOH HOH . F 6 HOH A 10 2010 2010 HOH HOH . F 6 HOH A 11 2011 2011 HOH HOH . F 6 HOH A 12 2012 2012 HOH HOH . F 6 HOH A 13 2013 2013 HOH HOH . F 6 HOH A 14 2014 2014 HOH HOH . F 6 HOH A 15 2015 2015 HOH HOH . F 6 HOH A 16 2016 2016 HOH HOH . G 6 HOH B 1 2001 2001 HOH HOH . G 6 HOH B 2 2002 2002 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 PB GDP . . . C 3 0.378 41.664 -6.446 1 47.89 ? PB GDP 1348 A 1 HETATM 2 O O1B GDP . . . C 3 1.764 41.704 -7.048 1 47.08 ? O1B GDP 1348 A 1 HETATM 3 O O2B GDP . . . C 3 0.427 42.096 -5 1 45.77 ? O2B GDP 1348 A 1 HETATM 4 O O3B GDP . . . C 3 -0.162 40.262 -6.596 1 46.8 ? O3B GDP 1348 A 1 HETATM 5 O O3A GDP . . . C 3 -0.57 42.72 -7.22 1 48.53 ? O3A GDP 1348 A 1 HETATM 6 P PA GDP . . . C 3 -1.969 42.322 -7.918 1 49.03 ? PA GDP 1348 A 1 HETATM 7 O O1A GDP . . . C 3 -3.001 41.981 -6.861 1 48.07 ? O1A GDP 1348 A 1 HETATM 8 O O2A GDP . . . C 3 -1.757 41.185 -8.897 1 48.56 ? O2A GDP 1348 A 1 HETATM 9 O O5' GDP . . . C 3 -2.395 43.66 -8.702 1 47.43 ? O5' GDP 1348 A 1 HETATM 10 C C5' GDP . . . C 3 -2.57 44.88 -7.989 1 47.08 ? C5' GDP 1348 A 1 HETATM 11 C C4' GDP . . . C 3 -3.639 45.733 -8.653 1 47.3 ? C4' GDP 1348 A 1 HETATM 12 O O4' GDP . . . C 3 -3.167 46.254 -9.906 1 47.59 ? O4' GDP 1348 A 1 HETATM 13 C C3' GDP . . . C 3 -4.903 44.942 -8.943 1 47.16 ? C3' GDP 1348 A 1 HETATM 14 O O3' GDP . . . C 3 -6.059 45.747 -8.662 1 46.58 ? O3' GDP 1348 A 1 HETATM 15 C C2' GDP . . . C 3 -4.797 44.618 -10.422 1 47.47 ? C2' GDP 1348 A 1 HETATM 16 O O2' GDP . . . C 3 -6.09 44.493 -11.014 1 46.22 ? O2' GDP 1348 A 1 HETATM 17 C C1' GDP . . . C 3 -4.002 45.795 -10.975 1 48.39 ? C1' GDP 1348 A 1 HETATM 18 N N9 GDP . . . C 3 -3.116 45.486 -12.12 1 50.36 ? N9 GDP 1348 A 1 HETATM 19 C C8 GDP . . . C 3 -2.152 44.541 -12.17 1 51.59 ? C8 GDP 1348 A 1 HETATM 20 N N7 GDP . . . C 3 -1.512 44.555 -13.374 1 51.65 ? N7 GDP 1348 A 1 HETATM 21 C C5 GDP . . . C 3 -2.063 45.541 -14.098 1 52.61 ? C5 GDP 1348 A 1 HETATM 22 C C6 GDP . . . C 3 -1.866 46.102 -15.446 1 54.34 ? C6 GDP 1348 A 1 HETATM 23 O O6 GDP . . . C 3 -0.99 45.63 -16.209 1 55.75 ? O6 GDP 1348 A 1 HETATM 24 N N1 GDP . . . C 3 -2.656 47.117 -15.825 1 55.08 ? N1 GDP 1348 A 1 HETATM 25 C C2 GDP . . . C 3 -3.605 47.638 -15.021 1 54.47 ? C2 GDP 1348 A 1 HETATM 26 N N2 GDP . . . C 3 -4.367 48.67 -15.459 1 53.95 ? N2 GDP 1348 A 1 HETATM 27 N N3 GDP . . . C 3 -3.837 47.168 -13.774 1 53.1 ? N3 GDP 1348 A 1 HETATM 28 C C4 GDP . . . C 3 -3.113 46.147 -13.272 1 51.7 ? C4 GDP 1348 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #