data_7V5I # _model_server_result.job_id rTIlYbuGM2Mf2w56EQ44Kw _model_server_result.datetime_utc '2024-11-25 20:44:30' _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 7v5i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":500}' # _entry.id 7V5I # _exptl.entry_id 7V5I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 90 _cell.entry_id 7V5I _cell.length_a 63.121 _cell.length_b 136.238 _cell.length_c 219.254 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7V5I _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,I,J 1 1 C,D,G,H 2 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 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 N1 C2 PLP doub 260 n y N1 C6 PLP sing 261 n y C2 C2A PLP sing 262 n n C2 C3 PLP sing 263 n y C2A H2A1 PLP sing 264 n n C2A H2A2 PLP sing 265 n n C2A H2A3 PLP sing 266 n n C3 O3 PLP sing 267 n n C3 C4 PLP doub 268 n y O3 HO3 PLP sing 269 n n C4 C4A PLP sing 270 n n C4 C5 PLP sing 271 n y C4A O4A PLP doub 272 n n C4A H4A PLP sing 273 n n C5 C6 PLP doub 274 n y C5 C5A PLP sing 275 n n C6 H6 PLP sing 276 n n C5A O4P PLP sing 277 n n C5A H5A1 PLP sing 278 n n C5A H5A2 PLP sing 279 n n O4P P PLP sing 280 n n P O1P PLP doub 281 n n P O2P PLP sing 282 n n P O3P PLP sing 283 n n O2P HOP2 PLP sing 284 n n O3P HOP3 PLP sing 285 n n # _atom_sites.entry_id 7V5I _atom_sites.fract_transf_matrix[1][1] 0.015843 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00734 _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] 0.004561 _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 PLP A 1 500 500 PLP PLP . F 2 PLP B 1 500 500 PLP PLP . G 2 PLP C 1 500 500 PLP PLP . H 2 PLP D 1 500 500 PLP PLP . I 3 HOH A 1 601 48 HOH HOH . I 3 HOH A 2 602 51 HOH HOH . I 3 HOH A 3 603 26 HOH HOH . I 3 HOH A 4 604 32 HOH HOH . I 3 HOH A 5 605 34 HOH HOH . I 3 HOH A 6 606 25 HOH HOH . I 3 HOH A 7 607 22 HOH HOH . I 3 HOH A 8 608 14 HOH HOH . I 3 HOH A 9 609 24 HOH HOH . I 3 HOH A 10 610 20 HOH HOH . I 3 HOH A 11 611 29 HOH HOH . I 3 HOH A 12 612 52 HOH HOH . I 3 HOH A 13 613 18 HOH HOH . I 3 HOH A 14 614 19 HOH HOH . I 3 HOH A 15 615 37 HOH HOH . I 3 HOH A 16 616 1 HOH HOH . I 3 HOH A 17 617 9 HOH HOH . I 3 HOH A 18 618 6 HOH HOH . I 3 HOH A 19 619 31 HOH HOH . I 3 HOH A 20 620 7 HOH HOH . I 3 HOH A 21 621 8 HOH HOH . I 3 HOH A 22 622 3 HOH HOH . I 3 HOH A 23 623 40 HOH HOH . I 3 HOH A 24 624 10 HOH HOH . J 3 HOH B 1 601 49 HOH HOH . J 3 HOH B 2 602 45 HOH HOH . J 3 HOH B 3 603 46 HOH HOH . J 3 HOH B 4 604 17 HOH HOH . J 3 HOH B 5 605 12 HOH HOH . J 3 HOH B 6 606 44 HOH HOH . J 3 HOH B 7 607 33 HOH HOH . J 3 HOH B 8 608 15 HOH HOH . J 3 HOH B 9 609 28 HOH HOH . J 3 HOH B 10 610 53 HOH HOH . J 3 HOH B 11 611 50 HOH HOH . J 3 HOH B 12 612 41 HOH HOH . J 3 HOH B 13 613 13 HOH HOH . J 3 HOH B 14 614 16 HOH HOH . J 3 HOH B 15 615 11 HOH HOH . J 3 HOH B 16 616 36 HOH HOH . J 3 HOH B 17 617 30 HOH HOH . J 3 HOH B 18 618 27 HOH HOH . J 3 HOH B 19 619 35 HOH HOH . J 3 HOH B 20 620 4 HOH HOH . J 3 HOH B 21 621 39 HOH HOH . J 3 HOH B 22 622 47 HOH HOH . J 3 HOH B 23 623 5 HOH HOH . J 3 HOH B 24 624 23 HOH HOH . J 3 HOH B 25 625 38 HOH HOH . J 3 HOH B 26 626 43 HOH HOH . J 3 HOH B 27 627 2 HOH HOH . J 3 HOH B 28 628 42 HOH HOH . J 3 HOH B 29 629 21 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 N N1 PLP . . . F 2 36.471 68.504 43.999 1 82.73 ? N1 PLP 500 B 1 HETATM 2 C C2 PLP . . . F 2 36.674 69.857 43.8 1 91.91 ? C2 PLP 500 B 1 HETATM 3 C C2A PLP . . . F 2 38.021 70.467 44.062 1 60.21 ? C2A PLP 500 B 1 HETATM 4 C C3 PLP . . . F 2 35.631 70.66 43.357 1 107.87 ? C3 PLP 500 B 1 HETATM 5 O O3 PLP . . . F 2 35.836 72.001 43.162 1 106.16 ? O3 PLP 500 B 1 HETATM 6 C C4 PLP . . . F 2 34.38 70.102 43.109 1 120.6 ? C4 PLP 500 B 1 HETATM 7 C C4A PLP . . . F 2 33.235 70.981 42.686 1 128.12 ? C4A PLP 500 B 1 HETATM 8 C C5 PLP . . . F 2 34.183 68.738 43.31 1 103.45 ? C5 PLP 500 B 1 HETATM 9 C C6 PLP . . . F 2 35.233 67.947 43.758 1 82.84 ? C6 PLP 500 B 1 HETATM 10 C C5A PLP . . . F 2 32.829 68.122 43.052 1 101.35 ? C5A PLP 500 B 1 HETATM 11 O O4P PLP . . . F 2 32.97 67.01 42.204 1 89.77 ? O4P PLP 500 B 1 HETATM 12 P P PLP . . . F 2 31.667 66.284 41.603 1 63.39 ? P PLP 500 B 1 HETATM 13 O O1P PLP . . . F 2 30.971 67.258 40.677 1 52.14 ? O1P PLP 500 B 1 HETATM 14 O O2P PLP . . . F 2 30.737 65.877 42.72 1 79.75 ? O2P PLP 500 B 1 HETATM 15 O O3P PLP . . . F 2 32.087 65.064 40.824 1 61.56 ? O3P PLP 500 B 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #