data_4X5B # _model_server_result.job_id 4fE7eR_qk_xMFPdQUC3gyA _model_server_result.datetime_utc '2024-11-18 02:27:21' _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 4x5b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4X5B # _exptl.entry_id 4X5B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 390.07 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 110.53 _cell.angle_gamma 90 _cell.entry_id 4X5B _cell.length_a 94.42 _cell.length_b 78.13 _cell.length_c 100.43 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4X5B _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _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,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D 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 OD2 ASP 111 B ASP 111 1_555 F MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc2 B OG SER 119 B SER 119 1_555 E MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc3 B OD1 ASP 251 B ASP 251 1_555 F MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc4 B OE2 GLU 252 B GLU 252 1_555 E MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc5 B OE2 GLU 252 B GLU 252 1_555 F MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc6 D O2A PRP . B PRP 401 1_555 E MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc7 D O1B PRP . B PRP 401 1_555 E MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc8 E MG MG . B MG 402 1_555 H O HOH . B HOH 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? metalc ? metalc9 E MG MG . B MG 402 1_555 H O HOH . B HOH 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc10 F MG MG . B MG 403 1_555 H O HOH . B HOH 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc11 F MG MG . B MG 403 1_555 H O HOH . B HOH 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc12 F MG MG . B MG 403 1_555 H O HOH . B HOH 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.874 ? # _chem_comp.formula 'C5 H13 O14 P3' _chem_comp.formula_weight 390.07 _chem_comp.id PRP _chem_comp.mon_nstd_flag n _chem_comp.name 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID;1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose;1-O-pyrophosphono-5-O-phosphono-D-ribose;1-O-pyrophosphono-5-O-phosphono-ribose' # 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 C1 C2 PRP sing 277 n n C1 O1 PRP sing 278 n n C1 O4 PRP sing 279 n n C1 H1 PRP sing 280 n n C2 C3 PRP sing 281 n n C2 O2 PRP sing 282 n n C2 H2 PRP sing 283 n n C3 C4 PRP sing 284 n n C3 O3 PRP sing 285 n n C3 H3 PRP sing 286 n n C4 C5 PRP sing 287 n n C4 O4 PRP sing 288 n n C4 H4 PRP sing 289 n n C5 O5 PRP sing 290 n n C5 H51 PRP sing 291 n n C5 H52 PRP sing 292 n n O1 PA PRP sing 293 n n O2 HO2 PRP sing 294 n n O3 HO3 PRP sing 295 n n O5 P PRP sing 296 n n P O1P PRP doub 297 n n P O2P PRP sing 298 n n P O3P PRP sing 299 n n O2P HOP2 PRP sing 300 n n O3P HOP3 PRP sing 301 n n PA O1A PRP doub 302 n n PA O2A PRP sing 303 n n PA O3A PRP sing 304 n n O2A HOA2 PRP sing 305 n n O3A PB PRP sing 306 n n PB O1B PRP doub 307 n n PB O2B PRP sing 308 n n PB O3B PRP sing 309 n n O2B HOB2 PRP sing 310 n n O3B HOB3 PRP sing 311 n n # _pdbx_chem_comp_identifier.comp_id PRP _pdbx_chem_comp_identifier.identifier a-D-Ribf1PO35PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 4X5B _atom_sites.fract_transf_matrix[1][1] 0.010591 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003966 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012799 _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] 0.010632 _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 2 PRP A 1 401 401 PRP PRP . D 2 PRP B 1 401 401 PRP PRP . E 3 MG B 1 402 402 MG MG . F 3 MG B 1 403 403 MG MG . G 4 HOH A 1 501 501 HOH HOH . G 4 HOH A 2 502 502 HOH HOH . G 4 HOH A 3 503 503 HOH HOH . G 4 HOH A 4 504 504 HOH HOH . G 4 HOH A 5 505 505 HOH HOH . G 4 HOH A 6 506 506 HOH HOH . G 4 HOH A 7 507 507 HOH HOH . G 4 HOH A 8 508 508 HOH HOH . G 4 HOH A 9 509 509 HOH HOH . G 4 HOH A 10 510 510 HOH HOH . G 4 HOH A 11 511 511 HOH HOH . G 4 HOH A 12 512 512 HOH HOH . G 4 HOH A 13 513 513 HOH HOH . G 4 HOH A 14 514 514 HOH HOH . G 4 HOH A 15 515 515 HOH HOH . G 4 HOH A 16 516 516 HOH HOH . G 4 HOH A 17 517 517 HOH HOH . G 4 HOH A 18 518 518 HOH HOH . G 4 HOH A 19 519 519 HOH HOH . G 4 HOH A 20 520 520 HOH HOH . G 4 HOH A 21 521 521 HOH HOH . G 4 HOH A 22 522 522 HOH HOH . G 4 HOH A 23 523 523 HOH HOH . H 4 HOH B 1 501 501 HOH HOH . H 4 HOH B 2 502 502 HOH HOH . H 4 HOH B 3 503 503 HOH HOH . H 4 HOH B 4 504 504 HOH HOH . H 4 HOH B 5 505 505 HOH HOH . H 4 HOH B 6 506 506 HOH HOH . H 4 HOH B 7 507 507 HOH HOH . H 4 HOH B 8 508 508 HOH HOH . H 4 HOH B 9 509 509 HOH HOH . H 4 HOH B 10 510 510 HOH HOH . H 4 HOH B 11 511 511 HOH HOH . H 4 HOH B 12 512 512 HOH HOH . H 4 HOH B 13 513 513 HOH HOH . H 4 HOH B 14 514 514 HOH HOH . H 4 HOH B 15 515 515 HOH HOH . H 4 HOH B 16 516 516 HOH HOH . H 4 HOH B 17 517 517 HOH HOH . H 4 HOH B 18 518 518 HOH HOH . H 4 HOH B 19 519 519 HOH HOH . H 4 HOH B 20 520 520 HOH HOH . H 4 HOH B 21 521 521 HOH HOH . H 4 HOH B 22 522 522 HOH HOH . H 4 HOH B 23 523 523 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 C C1 PRP . . . C 2 42.262 -50.344 35.784 0.5 51 ? C1 PRP 401 A 1 HETATM 2 C C2 PRP . . . C 2 41.029 -49.473 35.837 0.5 51.58 ? C2 PRP 401 A 1 HETATM 3 C C3 PRP . . . C 2 39.949 -50.511 35.627 0.5 52.66 ? C3 PRP 401 A 1 HETATM 4 C C4 PRP . . . C 2 40.62 -51.598 34.795 0.5 53.16 ? C4 PRP 401 A 1 HETATM 5 C C5 PRP . . . C 2 40.01 -51.685 33.404 0.5 54.21 ? C5 PRP 401 A 1 HETATM 6 O O1 PRP . . . C 2 42.316 -51.056 37.015 0.5 48.98 ? O1 PRP 401 A 1 HETATM 7 O O2 PRP . . . C 2 40.888 -48.794 37.087 0.5 51.12 ? O2 PRP 401 A 1 HETATM 8 O O3 PRP . . . C 2 39.501 -51.029 36.885 0.5 52.19 ? O3 PRP 401 A 1 HETATM 9 O O4 PRP . . . C 2 42.012 -51.268 34.729 0.5 52.26 ? O4 PRP 401 A 1 HETATM 10 O O5 PRP . . . C 2 40.324 -50.512 32.659 0.5 55.13 ? O5 PRP 401 A 1 HETATM 11 P P PRP . . . C 2 39.192 -49.815 31.753 0.5 56.31 ? P PRP 401 A 1 HETATM 12 O O1P PRP . . . C 2 39.835 -49.687 30.393 0.5 56.09 ? O1P PRP 401 A 1 HETATM 13 O O2P PRP . . . C 2 38.933 -48.499 32.448 0.5 55.88 ? O2P PRP 401 A 1 HETATM 14 O O3P PRP . . . C 2 38.043 -50.792 31.807 0.5 56.86 ? O3P PRP 401 A 1 HETATM 15 P PA PRP . . . C 2 43.622 -51.862 37.484 0.5 46.54 ? PA PRP 401 A 1 HETATM 16 O O1A PRP . . . C 2 44.78 -50.909 37.422 0.5 46.6 ? O1A PRP 401 A 1 HETATM 17 O O2A PRP . . . C 2 43.31 -52.602 38.76 0.5 47.18 ? O2A PRP 401 A 1 HETATM 18 O O3A PRP . . . C 2 43.841 -52.936 36.313 0.5 47.61 ? O3A PRP 401 A 1 HETATM 19 P PB PRP . . . C 2 45.097 -52.73 35.333 0.5 47.69 ? PB PRP 401 A 1 HETATM 20 O O1B PRP . . . C 2 44.537 -51.84 34.251 0.5 47.59 ? O1B PRP 401 A 1 HETATM 21 O O2B PRP . . . C 2 45.462 -54.123 34.914 0.5 47.8 ? O2B PRP 401 A 1 HETATM 22 O O3B PRP . . . C 2 46.132 -52.108 36.227 0.5 46.67 ? O3B PRP 401 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 384 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 22 #