data_4ACB # _model_server_result.job_id PV1mNuPDRDzQ6rxV3q5EeA _model_server_result.datetime_utc '2025-04-23 05:10:25' _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":"E","auth_seq_id":1469}' # _entry.id 4ACB # _exptl.entry_id 4ACB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 2 _struct_asym.id E _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 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 O1G GNP doub 289 n n PG O2G GNP sing 290 n n PG O3G GNP sing 291 n n PG N3B GNP sing 292 n n O2G HOG2 GNP sing 293 n n O3G HOG3 GNP sing 294 n n N3B PB GNP sing 295 n n N3B HNB3 GNP sing 296 n n PB O1B GNP doub 297 n n PB O2B GNP sing 298 n n PB O3A GNP sing 299 n n O2B HOB2 GNP sing 300 n n O3A PA GNP sing 301 n n PA O1A GNP doub 302 n n PA O2A GNP sing 303 n n PA O5' GNP sing 304 n n O2A HOA2 GNP sing 305 n n O5' C5' GNP sing 306 n n C5' C4' GNP sing 307 n n C5' "H5'2" GNP sing 308 n n C5' "H5'1" GNP sing 309 n n C4' O4' GNP sing 310 n n C4' C3' GNP sing 311 n n C4' H4' GNP sing 312 n n O4' C1' GNP sing 313 n n C3' O3' GNP sing 314 n n C3' C2' GNP sing 315 n n C3' H3' GNP sing 316 n n O3' HO3' GNP sing 317 n n C2' O2' GNP sing 318 n n C2' C1' GNP sing 319 n n C2' H2' GNP sing 320 n n O2' HO2' GNP sing 321 n n C1' N9 GNP sing 322 n n C1' H1' GNP sing 323 n n N9 C8 GNP sing 324 n y N9 C4 GNP sing 325 n y C8 N7 GNP doub 326 n y C8 H8 GNP sing 327 n n N7 C5 GNP sing 328 n y C5 C6 GNP sing 329 n y C5 C4 GNP doub 330 n y C6 O6 GNP doub 331 n n C6 N1 GNP sing 332 n y N1 C2 GNP sing 333 n y N1 HN1 GNP sing 334 n n C2 N2 GNP sing 335 n n C2 N3 GNP doub 336 n y N2 HN21 GNP sing 337 n n N2 HN22 GNP sing 338 n n N3 C4 GNP sing 339 n y # _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 PG GNP . . . E 2 23.424 -48.024 -43.643 1 191.47 ? PG GNP 1469 A 1 HETATM 2 O O1G GNP . . . E 2 23.69 -46.978 -42.583 1 202.13 ? O1G GNP 1469 A 1 HETATM 3 O O2G GNP . . . E 2 22.769 -47.553 -44.918 1 146.01 ? O2G GNP 1469 A 1 HETATM 4 O O3G GNP . . . E 2 22.709 -49.133 -42.908 1 202.09 ? O3G GNP 1469 A 1 HETATM 5 N N3B GNP . . . E 2 24.799 -48.638 -44.118 1 249.88 ? N3B GNP 1469 A 1 HETATM 6 P PB GNP . . . E 2 25.961 -47.724 -44.68 1 161.2 ? PB GNP 1469 A 1 HETATM 7 O O1B GNP . . . E 2 25.502 -46.961 -45.859 1 129.87 ? O1B GNP 1469 A 1 HETATM 8 O O2B GNP . . . E 2 26.46 -46.947 -43.517 1 184.61 ? O2B GNP 1469 A 1 HETATM 9 O O3A GNP . . . E 2 27.033 -48.683 -45.191 1 154.59 ? O3A GNP 1469 A 1 HETATM 10 P PA GNP . . . E 2 28.252 -49.074 -44.372 1 164.21 ? PA GNP 1469 A 1 HETATM 11 O O1A GNP . . . E 2 29.183 -47.929 -44.442 1 165.13 ? O1A GNP 1469 A 1 HETATM 12 O O2A GNP . . . E 2 27.852 -49.548 -43.031 1 191.75 ? O2A GNP 1469 A 1 HETATM 13 O O5' GNP . . . E 2 28.96 -50.298 -45.08 1 120.92 ? O5' GNP 1469 A 1 HETATM 14 C C5' GNP . . . E 2 28.249 -51.496 -45.38 1 146.1 ? C5' GNP 1469 A 1 HETATM 15 C C4' GNP . . . E 2 29.169 -52.575 -45.937 1 167.38 ? C4' GNP 1469 A 1 HETATM 16 O O4' GNP . . . E 2 29.905 -52.039 -47.067 1 174.82 ? O4' GNP 1469 A 1 HETATM 17 C C3' GNP . . . E 2 30.222 -53.124 -44.976 1 159.9 ? C3' GNP 1469 A 1 HETATM 18 O O3' GNP . . . E 2 30.423 -54.517 -45.188 1 148.67 ? O3' GNP 1469 A 1 HETATM 19 C C2' GNP . . . E 2 31.478 -52.368 -45.374 1 164.38 ? C2' GNP 1469 A 1 HETATM 20 O O2' GNP . . . E 2 32.643 -53.11 -45.076 1 187.52 ? O2' GNP 1469 A 1 HETATM 21 C C1' GNP . . . E 2 31.289 -52.251 -46.883 1 171.54 ? C1' GNP 1469 A 1 HETATM 22 N N9 GNP . . . E 2 32.043 -51.128 -47.432 1 169.04 ? N9 GNP 1469 A 1 HETATM 23 C C8 GNP . . . E 2 31.806 -49.795 -47.198 1 171.14 ? C8 GNP 1469 A 1 HETATM 24 N N7 GNP . . . E 2 32.642 -48.998 -47.801 1 176.87 ? N7 GNP 1469 A 1 HETATM 25 C C5 GNP . . . E 2 33.496 -49.861 -48.476 1 181.48 ? C5 GNP 1469 A 1 HETATM 26 C C6 GNP . . . E 2 34.607 -49.567 -49.301 1 166.2 ? C6 GNP 1469 A 1 HETATM 27 O O6 GNP . . . E 2 35.061 -48.451 -49.599 1 131.58 ? O6 GNP 1469 A 1 HETATM 28 N N1 GNP . . . E 2 35.202 -50.727 -49.794 1 163.23 ? N1 GNP 1469 A 1 HETATM 29 C C2 GNP . . . E 2 34.775 -52.006 -49.522 1 151.52 ? C2 GNP 1469 A 1 HETATM 30 N N2 GNP . . . E 2 35.479 -52.995 -50.093 1 156.06 ? N2 GNP 1469 A 1 HETATM 31 N N3 GNP . . . E 2 33.735 -52.293 -48.749 1 146.02 ? N3 GNP 1469 A 1 HETATM 32 C C4 GNP . . . E 2 33.144 -51.176 -48.26 1 167.36 ? C4 GNP 1469 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 410 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #