data_1V8T # _model_server_result.job_id cSvaq98sFcolC4gOSsMklw _model_server_result.datetime_utc '2024-10-18 23:31:18' _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 1v8t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 1V8T # _exptl.entry_id 1V8T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 230.11 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description RIBOSE-5-PHOSPHATE _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 1V8T _cell.length_a 49.93 _cell.length_b 49.93 _cell.length_c 117.95 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1V8T _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_555 -x,-x+y,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 78.633333 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 metalc ? metalc1 A OE1 GLU 44 A GLU 44 5_665 D ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc2 A OE2 GLU 70 A GLU 70 1_555 D ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc3 A OE1 GLU 70 A GLU 70 1_555 D ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc4 A OE2 GLU 82 A GLU 82 1_555 C ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? # _chem_comp.formula 'C5 H11 O8 P' _chem_comp.formula_weight 230.11 _chem_comp.id R5P _chem_comp.mon_nstd_flag . _chem_comp.name RIBOSE-5-PHOSPHATE _chem_comp.type saccharide _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 C1 O1 R5P doub 264 n n C1 C2 R5P sing 265 n n C2 O2 R5P sing 266 n n C2 C3 R5P sing 267 n n C3 O3 R5P sing 268 n n C3 C4 R5P sing 269 n n C4 O4 R5P sing 270 n n C4 C5 R5P sing 271 n n C5 O5 R5P sing 272 n n O5 P R5P sing 273 n n P O1P R5P doub 274 n n P O2P R5P sing 275 n n P O3P R5P sing 276 n n C1 H11 R5P sing 277 n n C2 HC2 R5P sing 278 n n O2 HO2 R5P sing 279 n n C3 HC3 R5P sing 280 n n O3 HO3 R5P sing 281 n n C4 HC4 R5P sing 282 n n O4 HO4 R5P sing 283 n n C5 H51 R5P sing 284 n n C5 H52 R5P sing 285 n n O2P HOP2 R5P sing 286 n n O3P HOP3 R5P sing 287 n n # _atom_sites.entry_id 1V8T _atom_sites.fract_transf_matrix[1][1] 0.020028 _atom_sites.fract_transf_matrix[1][2] 0.011563 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023126 _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] 0.008478 _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 B 2 R5P A 1 601 601 R5P R5P . C 3 ZN A 1 300 300 ZN ZN2 . D 3 ZN A 1 301 301 ZN ZN2 . E 4 HOH A 1 602 1 HOH TIP . E 4 HOH A 2 603 2 HOH TIP . E 4 HOH A 3 604 3 HOH TIP . E 4 HOH A 4 605 5 HOH TIP . E 4 HOH A 5 606 6 HOH TIP . E 4 HOH A 6 607 7 HOH TIP . E 4 HOH A 7 608 9 HOH TIP . E 4 HOH A 8 609 10 HOH TIP . E 4 HOH A 9 610 11 HOH TIP . E 4 HOH A 10 611 12 HOH TIP . E 4 HOH A 11 612 13 HOH TIP . E 4 HOH A 12 613 14 HOH TIP . E 4 HOH A 13 614 15 HOH TIP . E 4 HOH A 14 615 16 HOH TIP . E 4 HOH A 15 616 17 HOH TIP . E 4 HOH A 16 617 18 HOH TIP . E 4 HOH A 17 618 19 HOH TIP . E 4 HOH A 18 619 20 HOH TIP . # 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 R5P . . . B 2 -8.022 13.127 31.653 1 39.24 ? C1 R5P 601 A 1 HETATM 2 O O1 R5P . . . B 2 -8.783 13.139 32.62 1 36.45 ? O1 R5P 601 A 1 HETATM 3 C C2 R5P . . . B 2 -6.514 12.947 31.837 1 41.58 ? C2 R5P 601 A 1 HETATM 4 O O2 R5P . . . B 2 -5.836 13.903 31.018 1 38.49 ? O2 R5P 601 A 1 HETATM 5 C C3 R5P . . . B 2 -6.079 11.521 31.478 1 44.89 ? C3 R5P 601 A 1 HETATM 6 O O3 R5P . . . B 2 -4.668 11.378 31.662 1 43.45 ? O3 R5P 601 A 1 HETATM 7 C C4 R5P . . . B 2 -6.453 11.075 30.06 1 48.91 ? C4 R5P 601 A 1 HETATM 8 O O4 R5P . . . B 2 -5.919 9.771 29.814 1 49.08 ? O4 R5P 601 A 1 HETATM 9 C C5 R5P . . . B 2 -5.946 12.026 28.974 1 52.02 ? C5 R5P 601 A 1 HETATM 10 O O5 R5P . . . B 2 -6.414 11.606 27.69 1 55.97 ? O5 R5P 601 A 1 HETATM 11 P P R5P . . . B 2 -6.449 12.659 26.472 1 59.14 ? P R5P 601 A 1 HETATM 12 O O1P R5P . . . B 2 -5.111 13.182 26.109 1 57.68 ? O1P R5P 601 A 1 HETATM 13 O O2P R5P . . . B 2 -7.155 11.895 25.243 1 58.22 ? O2P R5P 601 A 1 HETATM 14 O O3P R5P . . . B 2 -7.462 13.828 26.924 1 55.47 ? O3P R5P 601 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 357 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #