data_4ESV # _model_server_result.job_id ELsiUrhvb19HAEfY9bkw-A _model_server_result.datetime_utc '2025-08-31 08:45:00' _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 4esv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"VA","auth_seq_id":501}' # _entry.id 4ESV # _exptl.entry_id 4ESV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 10 _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 4ESV _cell.length_a 149.124 _cell.length_b 180.321 _cell.length_c 279.128 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ESV _symmetry.cell_setting ? _symmetry.Int_Tables_number 17 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA heptameric 7 author_and_software_defined_assembly 1 ? heptameric 7 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,E,F,G,H,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,AB,BB,CB,DB 1 1 B,I,J,K,L,M,N,O,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,EB 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 ? 6 Q N N ? 6 X N N ? 6 CA N N ? 6 GA N N ? 6 KA N N ? 6 MA N N ? 6 PA N N ? 6 TA N N ? 6 VA N N ? 6 XA N 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 C OG SER 213 A SER 213 1_555 U CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc2 C OG1 THR 217 A THR 217 1_555 R CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc3 C O SER 378 A SER 378 1_555 T CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.191 ? metalc ? metalc4 C OD2 ASP 391 A ASP 391 1_555 V CA CA . A CA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.092 ? metalc ? metalc5 Q O1B GDP . A GDP 502 1_555 R CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc6 Q O2' GDP . A GDP 502 1_555 U CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.102 ? metalc ? metalc7 E OG1 THR 217 C THR 217 1_555 Y CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc8 X O1B GDP . C GDP 501 1_555 Y CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc9 F OG1 THR 217 D THR 217 1_555 DA CA CA . D CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc10 F O ASN 285 D ASN 285 1_555 FA CA CA . D CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc11 CA O1B GDP . D GDP 501 1_555 DA CA CA . D CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc12 G OG1 THR 217 E THR 217 1_555 HA CA CA . E CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc13 GA O1B GDP . E GDP 501 1_555 HA CA CA . E CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc14 H OG1 THR 217 F THR 217 1_555 LA CA CA . F CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc15 KA O1B GDP . F GDP 501 1_555 LA CA CA . F CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc16 K OG1 THR 217 I THR 217 1_555 QA CA CA . I CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.853 ? metalc ? metalc17 PA O1B GDP . I GDP 501 1_555 QA CA CA . I CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc18 XA O1B GDP . L GDP 501 1_555 ZA CA CA . L CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? # _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 124 n n PB O2B GDP sing 125 n n PB O3B GDP sing 126 n n PB O3A GDP sing 127 n n O2B HOB2 GDP sing 128 n n O3B HOB3 GDP sing 129 n n O3A PA GDP sing 130 n n PA O1A GDP doub 131 n n PA O2A GDP sing 132 n n PA O5' GDP sing 133 n n O2A HOA2 GDP sing 134 n n O5' C5' GDP sing 135 n n C5' C4' GDP sing 136 n n C5' H5' GDP sing 137 n n C5' "H5''" GDP sing 138 n n C4' O4' GDP sing 139 n n C4' C3' GDP sing 140 n n C4' H4' GDP sing 141 n n O4' C1' GDP sing 142 n n C3' O3' GDP sing 143 n n C3' C2' GDP sing 144 n n C3' H3' GDP sing 145 n n O3' HO3' GDP sing 146 n n C2' O2' GDP sing 147 n n C2' C1' GDP sing 148 n n C2' H2' GDP sing 149 n n O2' HO2' GDP sing 150 n n C1' N9 GDP sing 151 n n C1' H1' GDP sing 152 n n N9 C8 GDP sing 153 n y N9 C4 GDP sing 154 n y C8 N7 GDP doub 155 n y C8 H8 GDP sing 156 n n N7 C5 GDP sing 157 n y C5 C6 GDP sing 158 n n C5 C4 GDP doub 159 n y C6 O6 GDP doub 160 n n C6 N1 GDP sing 161 n n N1 C2 GDP sing 162 n n N1 HN1 GDP sing 163 n n C2 N2 GDP sing 164 n n C2 N3 GDP doub 165 n n N2 HN21 GDP sing 166 n n N2 HN22 GDP sing 167 n n N3 C4 GDP sing 168 n n # _atom_sites.entry_id 4ESV _atom_sites.fract_transf_matrix[1][1] 0.006706 _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] 0.005546 _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] 0.003583 _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 O 4 MES W 1 101 9 MES MES . P 5 CA A 1 501 17 CA CA . Q 6 GDP A 1 502 1 GDP GDP . R 5 CA A 1 503 1 CA CA . S 7 ALF A 1 504 1 ALF ALF . T 5 CA A 1 505 6 CA CA . U 5 CA A 1 506 7 CA CA . V 5 CA A 1 507 12 CA CA . W 5 CA B 1 501 16 CA CA . X 6 GDP C 1 501 2 GDP GDP . Y 5 CA C 1 502 2 CA CA . Z 7 ALF C 1 503 2 ALF ALF . AA 7 ALF C 1 504 3 ALF ALF . BA 4 MES C 1 505 8 MES MES . CA 6 GDP D 1 501 3 GDP GDP . DA 5 CA D 1 502 3 CA CA . EA 7 ALF D 1 503 4 ALF ALF . FA 5 CA D 1 504 13 CA CA . GA 6 GDP E 1 501 4 GDP GDP . HA 5 CA E 1 502 4 CA CA . IA 7 ALF E 1 503 5 ALF ALF . JA 4 MES E 1 504 15 MES MES . KA 6 GDP F 1 501 5 GDP GDP . LA 5 CA F 1 502 5 CA CA . MA 6 GDP G 1 501 6 GDP GDP . NA 7 ALF G 1 502 6 ALF ALF . OA 5 CA G 1 503 14 CA CA . PA 6 GDP I 1 501 7 GDP GDP . QA 5 CA I 1 502 6 CA CA . RA 7 ALF I 1 503 7 ALF ALF . SA 4 MES I 1 504 1 MES MES . TA 6 GDP J 1 501 8 GDP GDP . UA 7 ALF J 1 502 8 ALF ALF . VA 6 GDP K 1 501 9 GDP GDP . WA 7 ALF K 1 502 9 ALF ALF . XA 6 GDP L 1 501 10 GDP GDP . YA 7 ALF L 1 502 10 ALF ALF . ZA 5 CA L 1 503 10 CA CA . AB 8 HOH A 1 601 3 HOH HOH . BB 8 HOH B 1 601 2 HOH HOH . CB 8 HOH D 1 601 11 HOH HOH . DB 8 HOH E 1 601 5 HOH HOH . EB 8 HOH K 1 601 4 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 . . . VA 6 127.574 28.923 -55.198 1 169.47 ? PB GDP 501 K 1 HETATM 2 O O1B GDP . . . VA 6 128.827 28.53 -54.442 1 165.02 ? O1B GDP 501 K 1 HETATM 3 O O2B GDP . . . VA 6 126.992 30.155 -54.528 1 171.03 ? O2B GDP 501 K 1 HETATM 4 O O3B GDP . . . VA 6 126.58 27.795 -55.085 1 171.22 ? O3B GDP 501 K 1 HETATM 5 O O3A GDP . . . VA 6 127.85 29.232 -56.765 1 172.96 ? O3A GDP 501 K 1 HETATM 6 P PA GDP . . . VA 6 127.788 28.102 -57.93 1 176.43 ? PA GDP 501 K 1 HETATM 7 O O1A GDP . . . VA 6 126.848 26.987 -57.541 1 178.4 ? O1A GDP 501 K 1 HETATM 8 O O2A GDP . . . VA 6 129.17 27.547 -58.206 1 173.72 ? O2A GDP 501 K 1 HETATM 9 O O5' GDP . . . VA 6 127.204 28.828 -59.251 1 174.03 ? O5' GDP 501 K 1 HETATM 10 C C5' GDP . . . VA 6 125.9 28.499 -59.741 1 174.87 ? C5' GDP 501 K 1 HETATM 11 C C4' GDP . . . VA 6 125.57 29.339 -60.966 1 175.23 ? C4' GDP 501 K 1 HETATM 12 O O4' GDP . . . VA 6 126.259 28.758 -62.063 1 174.56 ? O4' GDP 501 K 1 HETATM 13 C C3' GDP . . . VA 6 124.083 29.331 -61.327 1 177.29 ? C3' GDP 501 K 1 HETATM 14 O O3' GDP . . . VA 6 123.346 30.531 -61.004 1 173.43 ? O3' GDP 501 K 1 HETATM 15 C C2' GDP . . . VA 6 124.057 29.136 -62.819 1 178.4 ? C2' GDP 501 K 1 HETATM 16 O O2' GDP . . . VA 6 123.508 30.286 -63.464 1 182.68 ? O2' GDP 501 K 1 HETATM 17 C C1' GDP . . . VA 6 125.498 28.954 -63.248 1 182.69 ? C1' GDP 501 K 1 HETATM 18 N N9 GDP . . . VA 6 125.498 27.801 -64.185 1 193.84 ? N9 GDP 501 K 1 HETATM 19 C C8 GDP . . . VA 6 125.923 26.538 -63.98 1 196.77 ? C8 GDP 501 K 1 HETATM 20 N N7 GDP . . . VA 6 125.739 25.773 -65.096 1 198.95 ? N7 GDP 501 K 1 HETATM 21 C C5 GDP . . . VA 6 125.173 26.556 -66.041 1 200.49 ? C5 GDP 501 K 1 HETATM 22 C C6 GDP . . . VA 6 124.694 26.42 -67.446 1 199.83 ? C6 GDP 501 K 1 HETATM 23 O O6 GDP . . . VA 6 124.771 25.337 -68.053 1 199.89 ? O6 GDP 501 K 1 HETATM 24 N N1 GDP . . . VA 6 124.171 27.498 -68.055 1 202.69 ? N1 GDP 501 K 1 HETATM 25 C C2 GDP . . . VA 6 124.059 28.695 -67.438 1 204.72 ? C2 GDP 501 K 1 HETATM 26 N N2 GDP . . . VA 6 123.521 29.751 -68.095 1 208.22 ? N2 GDP 501 K 1 HETATM 27 N N3 GDP . . . VA 6 124.467 28.89 -66.162 1 204.37 ? N3 GDP 501 K 1 HETATM 28 C C4 GDP . . . VA 6 125.019 27.886 -65.43 1 200.5 ? C4 GDP 501 K 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 271 _model_server_stats.query_time_ms 591 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #