data_4D0M # _model_server_result.job_id '_BUjbLgii-E6KPldTQY2yA' _model_server_result.datetime_utc '2024-11-26 01:09:44' _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 4d0m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"PB","auth_seq_id":2000}' # _entry.id 4D0M # _exptl.entry_id 4D0M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _entity.pdbx_number_of_molecules 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.33 _cell.angle_gamma 90 _cell.entry_id 4D0M _cell.length_a 199.504 _cell.length_b 134.465 _cell.length_c 294.328 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D0M _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # 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 dodecameric 12 author_and_software_defined_assembly 1 PISA dodecameric 12 author_and_software_defined_assembly 2 PISA dodecameric 12 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,O,P,S,T,U,V,KA,LA,MA,NA,OA,PA,ZA,AB,BB,FB,GB,HB 1 1 G,H,I,J,K,L,M,N,Q,R,EA,FA,QA,RA,SA,TA,UA,VA,WA,XA,YA,CB,DB,EB 2 1 W,X,Y,Z,AA,BA,CA,DA,GA,HA,IA,JA,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB 3 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 ? 5 LA N N ? 5 OA N N ? 5 RA N N ? 5 UA N N ? 5 XA N N ? 5 AB N N ? 5 DB N N ? 5 GB N N ? 5 JB N N ? 5 MB N N ? 5 PB N N ? 5 SB 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 B OG SER 28 B SER 25 1_555 MA MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.759 ? metalc ? metalc2 LA O3G GSP . B GSP 2000 1_555 MA MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.761 ? metalc ? metalc3 LA O2B GSP . B GSP 2000 1_555 MA MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc4 OA O3G GSP . D GSP 2000 1_555 PA MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? metalc ? metalc5 OA O2B GSP . D GSP 2000 1_555 PA MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc6 H OG1 THR 46 H THR 43 1_555 SA MG MG . H MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.71 ? metalc ? metalc7 RA O3G GSP . H GSP 2000 1_555 SA MG MG . H MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.728 ? metalc ? metalc8 RA O2B GSP . H GSP 2000 1_555 SA MG MG . H MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc9 UA O3G GSP . J GSP 2000 1_555 VA MG MG . J MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? metalc ? metalc10 UA O2B GSP . J GSP 2000 1_555 VA MG MG . J MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc11 XA O3G GSP . N GSP 2000 1_555 YA MG MG . N MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.858 ? metalc ? metalc12 XA O2B GSP . N GSP 2000 1_555 YA MG MG . N MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc13 AB O3G GSP . P GSP 2000 1_555 BB MG MG . P MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? metalc ? metalc14 AB O2B GSP . P GSP 2000 1_555 BB MG MG . P MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc15 DB O3G GSP . R GSP 2000 1_555 EB MG MG . R MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.85 ? metalc ? metalc16 DB O2B GSP . R GSP 2000 1_555 EB MG MG . R MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc17 T OG1 THR 46 T THR 43 1_555 HB MG MG . T MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.808 ? metalc ? metalc18 GB O3G GSP . T GSP 2000 1_555 HB MG MG . T MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? metalc ? metalc19 GB O2B GSP . T GSP 2000 1_555 HB MG MG . T MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc20 JB O3G GSP . X GSP 2000 1_555 KB MG MG . X MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.874 ? metalc ? metalc21 JB O2B GSP . X GSP 2000 1_555 KB MG MG . X MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc22 MB O3G GSP . Z GSP 2000 1_555 NB MG MG . Z MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc23 MB O2B GSP . Z GSP 2000 1_555 NB MG MG . Z MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc24 PB O3G GSP . d GSP 2000 1_555 QB MG MG . d MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc25 PB O2B GSP . d GSP 2000 1_555 QB MG MG . d MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc26 SB O3G GSP . h GSP 2000 1_555 TB MG MG . h MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? metalc ? metalc27 SB O2B GSP . h GSP 2000 1_555 TB MG MG . h MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? # _chem_comp.formula 'C10 H16 N5 O13 P3 S' _chem_comp.formula_weight 539.246 _chem_comp.id GSP _chem_comp.mon_nstd_flag . _chem_comp.name "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 PG O3B GSP sing 170 n n PG S1G GSP doub 171 n n PG O2G GSP sing 172 n n PG O3G GSP sing 173 n n O3B PB GSP sing 174 n n O2G HOG2 GSP sing 175 n n O3G HOG3 GSP sing 176 n n PB O1B GSP doub 177 n n PB O2B GSP sing 178 n n PB O3A GSP sing 179 n n O2B HOB2 GSP sing 180 n n PA O1A GSP doub 181 n n PA O2A GSP sing 182 n n PA O3A GSP sing 183 n n PA O5' GSP sing 184 n n O2A HOA2 GSP sing 185 n n O5' C5' GSP sing 186 n n C5' C4' GSP sing 187 n n C5' "H5'1" GSP sing 188 n n C5' "H5'2" GSP sing 189 n n C4' O4' GSP sing 190 n n C4' C3' GSP sing 191 n n C4' H4' GSP sing 192 n n O4' C1' GSP sing 193 n n C3' O3' GSP sing 194 n n C3' C2' GSP sing 195 n n C3' H3' GSP sing 196 n n O3' HO3' GSP sing 197 n n C2' O2' GSP sing 198 n n C2' C1' GSP sing 199 n n C2' H2' GSP sing 200 n n O2' HO2' GSP sing 201 n n C1' N9 GSP sing 202 n n C1' H1' GSP sing 203 n n N9 C8 GSP sing 204 n y N9 C4 GSP sing 205 n y C8 N7 GSP doub 206 n y C8 H8 GSP sing 207 n n N7 C5 GSP sing 208 n y C5 C6 GSP sing 209 n n C5 C4 GSP doub 210 n y C6 O6 GSP doub 211 n n C6 N1 GSP sing 212 n n N1 C2 GSP sing 213 n n N1 HN1 GSP sing 214 n n C2 N2 GSP sing 215 n n C2 N3 GSP doub 216 n n N2 HN21 GSP sing 217 n n N2 HN22 GSP sing 218 n n N3 C4 GSP sing 219 n n # _atom_sites.entry_id 4D0M _atom_sites.fract_transf_matrix[1][1] 0.005012 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000029 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007437 _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] 0.003398 _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 KA 4 093 A 1 2002 2002 093 093 . LA 5 GSP B 1 2000 2000 GSP GSP . MA 6 MG B 1 2001 2001 MG MG . NA 4 093 C 1 2002 2002 093 093 . OA 5 GSP D 1 2000 2000 GSP GSP . PA 6 MG D 1 2001 2001 MG MG . QA 4 093 G 1 2002 2002 093 093 . RA 5 GSP H 1 2000 2000 GSP GSP . SA 6 MG H 1 2001 2001 MG MG . TA 4 093 I 1 2002 2002 093 093 . UA 5 GSP J 1 2000 2000 GSP GSP . VA 6 MG J 1 2001 2001 MG MG . WA 4 093 M 1 2002 2002 093 093 . XA 5 GSP N 1 2000 2000 GSP GSP . YA 6 MG N 1 2001 2001 MG MG . ZA 4 093 O 1 2002 2002 093 093 . AB 5 GSP P 1 2000 2000 GSP GSP . BB 6 MG P 1 2001 2001 MG MG . CB 4 093 Q 1 2002 2002 093 093 . DB 5 GSP R 1 2000 2000 GSP GSP . EB 6 MG R 1 2001 2001 MG MG . FB 4 093 S 1 2002 2002 093 093 . GB 5 GSP T 1 2000 2000 GSP GSP . HB 6 MG T 1 2001 2001 MG MG . IB 4 093 W 1 2002 2002 093 093 . JB 5 GSP X 1 2000 2000 GSP GSP . KB 6 MG X 1 2001 2001 MG MG . LB 4 093 Y 1 2002 2002 093 093 . MB 5 GSP Z 1 2000 2000 GSP GSP . NB 6 MG Z 1 2001 2001 MG MG . OB 4 093 c 1 2002 2002 093 093 . PB 5 GSP d 1 2000 2000 GSP GSP . QB 6 MG d 1 2001 2001 MG MG . RB 4 093 g 1 2002 2002 093 093 . SB 5 GSP h 1 2000 2000 GSP GSP . TB 6 MG h 1 2001 2001 MG MG . # 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 PG GSP . . . PB 5 102.942 215.809 69.092 1 349.98 ? PG GSP 2000 d 1 HETATM 2 O O3B GSP . . . PB 5 102.095 215.5 67.764 1 278.49 ? O3B GSP 2000 d 1 HETATM 3 S S1G GSP . . . PB 5 104.063 214.233 69.36 1 312.64 ? S1G GSP 2000 d 1 HETATM 4 O O2G GSP . . . PB 5 101.979 216.14 70.383 1 391.75 ? O2G GSP 2000 d 1 HETATM 5 O O3G GSP . . . PB 5 103.823 217.129 68.742 1 391.78 ? O3G GSP 2000 d 1 HETATM 6 P PB GSP . . . PB 5 101.437 216.796 67.077 1 280.72 ? PB GSP 2000 d 1 HETATM 7 O O1B GSP . . . PB 5 100.046 216.945 67.676 1 323.46 ? O1B GSP 2000 d 1 HETATM 8 O O2B GSP . . . PB 5 102.411 217.959 67.168 1 337.06 ? O2B GSP 2000 d 1 HETATM 9 P PA GSP . . . PB 5 102.575 216.147 64.609 1 206.5 ? PA GSP 2000 d 1 HETATM 10 O O1A GSP . . . PB 5 103.176 217.344 63.862 1 194.97 ? O1A GSP 2000 d 1 HETATM 11 O O2A GSP . . . PB 5 103.501 215.381 65.512 1 188.82 ? O2A GSP 2000 d 1 HETATM 12 O O3A GSP . . . PB 5 101.298 216.502 65.511 1 232.74 ? O3A GSP 2000 d 1 HETATM 13 O O5' GSP . . . PB 5 101.746 215.2 63.558 1 220.31 ? O5' GSP 2000 d 1 HETATM 14 C C5' GSP . . . PB 5 101.686 213.772 63.658 1 218.67 ? C5' GSP 2000 d 1 HETATM 15 C C4' GSP . . . PB 5 101.542 213.102 62.28 1 210.51 ? C4' GSP 2000 d 1 HETATM 16 O O4' GSP . . . PB 5 100.272 213.336 61.659 1 184.47 ? O4' GSP 2000 d 1 HETATM 17 C C3' GSP . . . PB 5 102.594 213.598 61.281 1 212.5 ? C3' GSP 2000 d 1 HETATM 18 O O3' GSP . . . PB 5 103.129 212.534 60.498 1 246.12 ? O3' GSP 2000 d 1 HETATM 19 C C2' GSP . . . PB 5 101.897 214.506 60.322 1 191.21 ? C2' GSP 2000 d 1 HETATM 20 O O2' GSP . . . PB 5 102.53 214.462 59.043 1 184.79 ? O2' GSP 2000 d 1 HETATM 21 C C1' GSP . . . PB 5 100.5 213.908 60.366 1 174.17 ? C1' GSP 2000 d 1 HETATM 22 N N9 GSP . . . PB 5 99.52 214.981 60.16 1 181.09 ? N9 GSP 2000 d 1 HETATM 23 C C8 GSP . . . PB 5 99.4 216.142 60.853 1 209.8 ? C8 GSP 2000 d 1 HETATM 24 N N7 GSP . . . PB 5 98.351 216.865 60.362 1 216.9 ? N7 GSP 2000 d 1 HETATM 25 C C5 GSP . . . PB 5 97.815 216.167 59.34 1 208.5 ? C5 GSP 2000 d 1 HETATM 26 C C6 GSP . . . PB 5 96.708 216.342 58.371 1 207.81 ? C6 GSP 2000 d 1 HETATM 27 O O6 GSP . . . PB 5 95.978 217.35 58.393 1 194.48 ? O6 GSP 2000 d 1 HETATM 28 N N1 GSP . . . PB 5 96.49 215.378 57.471 1 216.23 ? N1 GSP 2000 d 1 HETATM 29 C C2 GSP . . . PB 5 97.255 214.268 57.422 1 229.34 ? C2 GSP 2000 d 1 HETATM 30 N N2 GSP . . . PB 5 96.974 213.33 56.486 1 237.43 ? N2 GSP 2000 d 1 HETATM 31 N N3 GSP . . . PB 5 98.294 214.037 58.267 1 202.98 ? N3 GSP 2000 d 1 HETATM 32 C C4 GSP . . . PB 5 98.599 214.932 59.222 1 191.39 ? C4 GSP 2000 d 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 81 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 32 #