data_4ACB # _model_server_result.job_id 2Uj0LUbXS_5hS2_BtWQuWw _model_server_result.datetime_utc '2025-04-12 21:34:34' _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 4acb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1469}' # _entry.id 4ACB # _exptl.entry_id 4ACB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 4ACB _cell.length_a 146.63 _cell.length_b 146.63 _cell.length_c 297.22 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ACB _symmetry.cell_setting ? _symmetry.Int_Tables_number 151 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 1 2' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,W 1 1 B,G,H,I,J,K,L,X 2 1 C,M,N,O,P,Q,R,S,T,U,V 3 1 D 4 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 4 _struct_asym.id G _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 A C GLY 277 A GLY 263 1_555 A N CMH 278 A CMH 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C CMH 278 A CMH 264 1_555 A N ILE 279 A ILE 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C GLU 351 A GLU 337 1_555 A N CMH 352 A CMH 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C CMH 352 A CMH 338 1_555 A N TYR 353 A TYR 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 A C TYR 353 A TYR 339 1_555 A N CMH 354 A CMH 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale6 A C CMH 354 A CMH 340 1_555 A N ALA 355 A ALA 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale7 A C ILE 384 A ILE 370 1_555 A N CMH 385 A CMH 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale8 A C CMH 385 A CMH 371 1_555 A N GLY 386 A GLY 372 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale9 B C GLY 277 B GLY 263 1_555 B N CMH 278 B CMH 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale10 B C CMH 278 B CMH 264 1_555 B N ILE 279 B ILE 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale11 B C GLU 351 B GLU 337 1_555 B N CMH 352 B CMH 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale12 B C CMH 352 B CMH 338 1_555 B N TYR 353 B TYR 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale13 B C TYR 353 B TYR 339 1_555 B N CMH 354 B CMH 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 B C CMH 354 B CMH 340 1_555 B N ALA 355 B ALA 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale15 B C ILE 384 B ILE 370 1_555 B N CMH 385 B CMH 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale16 B C CMH 385 B CMH 371 1_555 B N GLY 386 B GLY 372 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale17 C C GLY 277 C GLY 263 1_555 C N CMH 278 C CMH 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale18 C C CMH 278 C CMH 264 1_555 C N ILE 279 C ILE 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale19 C C GLU 351 C GLU 337 1_555 C N CMH 352 C CMH 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale20 C C CMH 352 C CMH 338 1_555 C N TYR 353 C TYR 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale21 C C TYR 353 C TYR 339 1_555 C N CMH 354 C CMH 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.315 ? covale ? covale22 C C CMH 354 C CMH 340 1_555 C N ALA 355 C ALA 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale23 C C ILE 384 C ILE 370 1_555 C N CMH 385 C CMH 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale24 C C CMH 385 C CMH 371 1_555 C N GLY 386 C GLY 372 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale25 D C GLY 277 D GLY 263 1_555 D N CMH 278 D CMH 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale26 D C CMH 278 D CMH 264 1_555 D N ILE 279 D ILE 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale27 D C GLU 351 D GLU 337 1_555 D N CMH 352 D CMH 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale28 D C CMH 352 D CMH 338 1_555 D N TYR 353 D TYR 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale29 D C TYR 353 D TYR 339 1_555 D N CMH 354 D CMH 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale30 D C CMH 354 D CMH 340 1_555 D N ALA 355 D ALA 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale31 D C ILE 384 D ILE 370 1_555 D N CMH 385 D CMH 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale32 D C CMH 385 D CMH 371 1_555 D N GLY 386 D GLY 372 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OG1 THR 33 A THR 19 1_555 F MG MG . A MG 1470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc2 A OG1 THR 60 A THR 46 1_555 F MG MG . A MG 1470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc3 A O GLU 351 A GLU 337 1_555 A HG CMH 352 A CMH 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc4 E O1G GNP . A GNP 1469 1_555 F MG MG . A MG 1470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc5 E O2B GNP . A GNP 1469 1_555 F MG MG . A MG 1470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc6 F MG MG . A MG 1470 1_555 W O HOH . A HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc7 F MG MG . A MG 1470 1_555 W O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc8 B OG1 THR 33 B THR 19 1_555 H MG MG . B MG 1470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc9 B O GLU 351 B GLU 337 1_555 B HG CMH 352 B CMH 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.013 ? metalc ? metalc10 G O2B GDP . B GDP 1469 1_555 H MG MG . B MG 1470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc11 H MG MG . B MG 1470 1_555 X O HOH . B HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc12 H MG MG . B MG 1470 1_555 X O HOH . B HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc13 H MG MG . B MG 1470 1_555 X O HOH . B HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc14 H MG MG . B MG 1470 1_555 X O HOH . B HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc15 C O GLU 351 C GLU 337 1_555 C HG CMH 352 C CMH 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? metalc ? metalc16 D O GLY 277 D GLY 263 1_555 D HG CMH 278 D CMH 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.024 ? # _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 198 n n PB O2B GDP sing 199 n n PB O3B GDP sing 200 n n PB O3A GDP sing 201 n n O2B HOB2 GDP sing 202 n n O3B HOB3 GDP sing 203 n n O3A PA GDP sing 204 n n PA O1A GDP doub 205 n n PA O2A GDP sing 206 n n PA O5' GDP sing 207 n n O2A HOA2 GDP sing 208 n n O5' C5' GDP sing 209 n n C5' C4' GDP sing 210 n n C5' H5' GDP sing 211 n n C5' "H5''" GDP sing 212 n n C4' O4' GDP sing 213 n n C4' C3' GDP sing 214 n n C4' H4' GDP sing 215 n n O4' C1' GDP sing 216 n n C3' O3' GDP sing 217 n n C3' C2' GDP sing 218 n n C3' H3' GDP sing 219 n n O3' HO3' GDP sing 220 n n C2' O2' GDP sing 221 n n C2' C1' GDP sing 222 n n C2' H2' GDP sing 223 n n O2' HO2' GDP sing 224 n n C1' N9 GDP sing 225 n n C1' H1' GDP sing 226 n n N9 C8 GDP sing 227 n y N9 C4 GDP sing 228 n y C8 N7 GDP doub 229 n y C8 H8 GDP sing 230 n n N7 C5 GDP sing 231 n y C5 C6 GDP sing 232 n n C5 C4 GDP doub 233 n y C6 O6 GDP doub 234 n n C6 N1 GDP sing 235 n n N1 C2 GDP sing 236 n n N1 HN1 GDP sing 237 n n C2 N2 GDP sing 238 n n C2 N3 GDP doub 239 n n N2 HN21 GDP sing 240 n n N2 HN22 GDP sing 241 n n N3 C4 GDP sing 242 n n # _atom_sites.entry_id 4ACB _atom_sites.fract_transf_matrix[1][1] 0.00682 _atom_sites.fract_transf_matrix[1][2] 0.003937 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007875 _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] 0.003365 _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 E 2 GNP A 1 1469 1469 GNP GNP . F 3 MG A 1 1470 1470 MG MG . G 4 GDP B 1 1469 1469 GDP GDP . H 3 MG B 1 1470 1470 MG MG . I 5 SO4 B 1 1471 1471 SO4 SO4 . J 5 SO4 B 1 1472 1472 SO4 SO4 . K 6 DXC B 1 1473 1473 DXC DXC . L 7 5GP B 1 1474 1474 5GP 5GP . M 5 SO4 C 1 1471 1471 SO4 SO4 . N 5 SO4 C 1 1472 1472 SO4 SO4 . O 5 SO4 C 1 1473 1473 SO4 SO4 . P 6 DXC C 1 1475 1475 DXC DXC . Q 6 DXC C 1 1476 1476 DXC DXC . R 6 DXC C 1 1477 1477 DXC DXC . S 6 DXC C 1 1478 1478 DXC DXC . T 6 DXC C 1 1479 1479 DXC DXC . U 6 DXC C 1 1480 1480 DXC DXC . V 5 SO4 C 1 1481 1481 SO4 SO4 . W 8 HOH A 1 2001 2001 HOH HOH . W 8 HOH A 2 2002 2002 HOH HOH . X 8 HOH B 1 2001 2001 HOH HOH . X 8 HOH B 2 2002 2002 HOH HOH . X 8 HOH B 3 2003 2003 HOH HOH . X 8 HOH B 4 2004 2004 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 . . . G 4 49.074 -19.488 -18.146 0.9 180.54 ? PB GDP 1469 B 1 HETATM 2 O O1B GDP . . . G 4 47.565 -19.474 -18.095 0.9 127.32 ? O1B GDP 1469 B 1 HETATM 3 O O2B GDP . . . G 4 49.563 -19.809 -16.753 0.9 197.49 ? O2B GDP 1469 B 1 HETATM 4 O O3B GDP . . . G 4 49.519 -20.569 -19.103 0.9 210.25 ? O3B GDP 1469 B 1 HETATM 5 O O3A GDP . . . G 4 49.618 -18.035 -18.617 0.9 126.27 ? O3A GDP 1469 B 1 HETATM 6 P PA GDP . . . G 4 50.67 -17.789 -19.827 0.9 197.77 ? PA GDP 1469 B 1 HETATM 7 O O1A GDP . . . G 4 51.586 -16.632 -19.495 0.9 197.51 ? O1A GDP 1469 B 1 HETATM 8 O O2A GDP . . . G 4 51.509 -19.005 -20.152 0.9 203.06 ? O2A GDP 1469 B 1 HETATM 9 O O5' GDP . . . G 4 49.744 -17.364 -21.075 0.9 181.72 ? O5' GDP 1469 B 1 HETATM 10 C C5' GDP . . . G 4 49.827 -18.078 -22.307 0.9 198.5 ? C5' GDP 1469 B 1 HETATM 11 C C4' GDP . . . G 4 50.324 -17.131 -23.386 0.9 204.69 ? C4' GDP 1469 B 1 HETATM 12 O O4' GDP . . . G 4 49.654 -15.88 -23.248 0.9 205.37 ? O4' GDP 1469 B 1 HETATM 13 C C3' GDP . . . G 4 51.807 -16.861 -23.206 0.9 204.09 ? C3' GDP 1469 B 1 HETATM 14 O O3' GDP . . . G 4 52.49 -17.093 -24.441 0.9 195.29 ? O3' GDP 1469 B 1 HETATM 15 C C2' GDP . . . G 4 51.912 -15.398 -22.826 0.9 207.05 ? C2' GDP 1469 B 1 HETATM 16 O O2' GDP . . . G 4 53.031 -14.8 -23.484 0.9 212.31 ? O2' GDP 1469 B 1 HETATM 17 C C1' GDP . . . G 4 50.594 -14.807 -23.298 0.9 199.12 ? C1' GDP 1469 B 1 HETATM 18 N N9 GDP . . . G 4 50.091 -13.721 -22.427 0.9 180.33 ? N9 GDP 1469 B 1 HETATM 19 C C8 GDP . . . G 4 50.026 -13.737 -21.084 0.9 210.68 ? C8 GDP 1469 B 1 HETATM 20 N N7 GDP . . . G 4 49.487 -12.584 -20.609 0.9 235.38 ? N7 GDP 1469 B 1 HETATM 21 C C5 GDP . . . G 4 49.181 -11.812 -21.671 0.9 215.61 ? C5 GDP 1469 B 1 HETATM 22 C C6 GDP . . . G 4 48.581 -10.472 -21.888 0.9 202.95 ? C6 GDP 1469 B 1 HETATM 23 O O6 GDP . . . G 4 48.219 -9.764 -20.919 0.9 202.9 ? O6 GDP 1469 B 1 HETATM 24 N N1 GDP . . . G 4 48.438 -10.045 -23.153 0.9 173.2 ? N1 GDP 1469 B 1 HETATM 25 C C2 GDP . . . G 4 48.818 -10.785 -24.215 0.9 163.85 ? C2 GDP 1469 B 1 HETATM 26 N N2 GDP . . . G 4 48.64 -10.278 -25.463 0.9 159.22 ? N2 GDP 1469 B 1 HETATM 27 N N3 GDP . . . G 4 49.375 -12.018 -24.083 0.9 161.81 ? N3 GDP 1469 B 1 HETATM 28 C C4 GDP . . . G 4 49.578 -12.571 -22.864 0.9 174.43 ? C4 GDP 1469 B 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 387 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #