data_5LRB # _model_server_result.job_id svA9i9uJlsvQ5PuwnREECQ _model_server_result.datetime_utc '2024-11-27 00:30:02' _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 5lrb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1002}' # _entry.id 5LRB # _exptl.entry_id 5LRB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _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 115.07 _cell.angle_gamma 90 _cell.entry_id 5LRB _cell.length_a 230.33 _cell.length_b 63.68 _cell.length_c 149.33 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LRB _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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,C,E,F,I 1 1,2 B,D,G,H,J 2 1,3 # 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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 167.055114 0 135.261738 3 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 H N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 GLC GLC C1 O1 . O4 HO4 . sing 2 ? 2 3 2 AC1 GLC C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C GLC 1 C 1 GLC A 1003 ACR 2 n C GLC 2 C 2 GLC A 1003 ACR 2 n C AC1 3 C 3 AC1 A 1003 ACR 2 n D GLC 1 D 1 GLC B 1003 ACR 2 n D GLC 2 D 2 GLC B 1003 ACR 2 n D AC1 3 D 3 AC1 B 1003 ACR # 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 NZ LYS 772 A LYS 814 1_555 F C4A PLP . A PLP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.267 ? covale ? covale2 B NZ LYS 772 B LYS 814 1_555 H C4A PLP . B PLP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.261 ? covale ? covale3 C O4 GLC . C GLC 1 1_555 C C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 sing covale ? covale4 C O4 GLC . C GLC 2 1_555 C C1 AC1 . C AC1 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 sing covale ? covale5 D O4 GLC . D GLC 1 1_555 D C1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 sing covale ? covale6 D O4 GLC . D GLC 2 1_555 D C1 AC1 . D AC1 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 sing # _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 330 n y N1 C6 PLP sing 331 n y C2 C2A PLP sing 332 n n C2 C3 PLP sing 333 n y C2A H2A1 PLP sing 334 n n C2A H2A2 PLP sing 335 n n C2A H2A3 PLP sing 336 n n C3 O3 PLP sing 337 n n C3 C4 PLP doub 338 n y O3 HO3 PLP sing 339 n n C4 C4A PLP sing 340 n n C4 C5 PLP sing 341 n y C4A O4A PLP doub 342 n n C4A H4A PLP sing 343 n n C5 C6 PLP doub 344 n y C5 C5A PLP sing 345 n n C6 H6 PLP sing 346 n n C5A O4P PLP sing 347 n n C5A H5A1 PLP sing 348 n n C5A H5A2 PLP sing 349 n n O4P P PLP sing 350 n n P O1P PLP doub 351 n n P O2P PLP sing 352 n n P O3P PLP sing 353 n n O2P HOP2 PLP sing 354 n n O3P HOP3 PLP sing 355 n n # _atom_sites.entry_id 5LRB _atom_sites.fract_transf_matrix[1][1] 0.004342 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002031 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015704 _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] 0.007393 _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 3 GLC A 1 1001 1001 GLC GLC . F 4 PLP A 1 1002 1002 PLP PLP . G 3 GLC B 1 1001 1001 GLC GLC . H 4 PLP B 1 1002 1002 PLP PLP . I 5 HOH A 1 1101 1102 HOH HOH . I 5 HOH A 2 1102 1109 HOH HOH . I 5 HOH A 3 1103 1112 HOH HOH . I 5 HOH A 4 1104 1101 HOH HOH . I 5 HOH A 5 1105 1127 HOH HOH . I 5 HOH A 6 1106 1120 HOH HOH . I 5 HOH A 7 1107 1106 HOH HOH . I 5 HOH A 8 1108 1115 HOH HOH . I 5 HOH A 9 1109 1103 HOH HOH . I 5 HOH A 10 1110 1111 HOH HOH . I 5 HOH A 11 1111 1123 HOH HOH . I 5 HOH A 12 1112 1108 HOH HOH . I 5 HOH A 13 1113 1119 HOH HOH . I 5 HOH A 14 1114 1114 HOH HOH . I 5 HOH A 15 1115 1113 HOH HOH . I 5 HOH A 16 1116 1121 HOH HOH . I 5 HOH A 17 1117 1107 HOH HOH . I 5 HOH A 18 1118 1128 HOH HOH . I 5 HOH A 19 1119 1116 HOH HOH . I 5 HOH A 20 1120 1104 HOH HOH . I 5 HOH A 21 1121 1122 HOH HOH . I 5 HOH A 22 1122 1125 HOH HOH . I 5 HOH A 23 1123 1105 HOH HOH . I 5 HOH A 24 1124 1117 HOH HOH . I 5 HOH A 25 1125 1118 HOH HOH . I 5 HOH A 26 1126 1124 HOH HOH . I 5 HOH A 27 1127 1126 HOH HOH . I 5 HOH A 28 1128 1110 HOH HOH . J 5 HOH B 1 1101 1105 HOH HOH . J 5 HOH B 2 1102 1119 HOH HOH . J 5 HOH B 3 1103 1121 HOH HOH . J 5 HOH B 4 1104 1114 HOH HOH . J 5 HOH B 5 1105 1103 HOH HOH . J 5 HOH B 6 1106 1127 HOH HOH . J 5 HOH B 7 1107 1110 HOH HOH . J 5 HOH B 8 1108 1118 HOH HOH . J 5 HOH B 9 1109 1113 HOH HOH . J 5 HOH B 10 1110 1101 HOH HOH . J 5 HOH B 11 1111 1124 HOH HOH . J 5 HOH B 12 1112 1116 HOH HOH . J 5 HOH B 13 1113 1102 HOH HOH . J 5 HOH B 14 1114 1112 HOH HOH . J 5 HOH B 15 1115 1115 HOH HOH . J 5 HOH B 16 1116 1117 HOH HOH . J 5 HOH B 17 1117 1109 HOH HOH . J 5 HOH B 18 1118 1111 HOH HOH . J 5 HOH B 19 1119 1108 HOH HOH . J 5 HOH B 20 1120 1125 HOH HOH . J 5 HOH B 21 1121 1107 HOH HOH . J 5 HOH B 22 1122 1106 HOH HOH . J 5 HOH B 23 1123 1126 HOH HOH . J 5 HOH B 24 1124 1104 HOH HOH . J 5 HOH B 25 1125 1120 HOH HOH . J 5 HOH B 26 1126 1122 HOH HOH . J 5 HOH B 27 1127 1123 HOH HOH . J 5 HOH B 28 1128 1128 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 . . . H 4 26.11 4.7 11.17 1 60.21 ? N1 PLP 1002 B 1 HETATM 2 C C2 PLP . . . H 4 26.026 3.421 10.763 1 59.75 ? C2 PLP 1002 B 1 HETATM 3 C C2A PLP . . . H 4 25.457 3.12 9.408 1 62.32 ? C2A PLP 1002 B 1 HETATM 4 C C3 PLP . . . H 4 26.495 2.318 11.631 1 60.56 ? C3 PLP 1002 B 1 HETATM 5 O O3 PLP . . . H 4 26.426 1.016 11.238 1 62.27 ? O3 PLP 1002 B 1 HETATM 6 C C4 PLP . . . H 4 27.048 2.676 12.946 1 61.69 ? C4 PLP 1002 B 1 HETATM 7 C C4A PLP . . . H 4 27.531 1.621 13.858 1 61.43 ? C4A PLP 1002 B 1 HETATM 8 C C5 PLP . . . H 4 27.093 4.117 13.274 1 63.43 ? C5 PLP 1002 B 1 HETATM 9 C C6 PLP . . . H 4 26.614 5.048 12.359 1 63.88 ? C6 PLP 1002 B 1 HETATM 10 C C5A PLP . . . H 4 27.618 4.618 14.59 1 64.88 ? C5A PLP 1002 B 1 HETATM 11 O O4P PLP . . . H 4 28.936 5.126 14.448 1 68.5 ? O4P PLP 1002 B 1 HETATM 12 P P PLP . . . H 4 29.501 6.106 15.6 1 75.5 ? P PLP 1002 B 1 HETATM 13 O O1P PLP . . . H 4 29.477 7.464 14.906 1 69.33 ? O1P PLP 1002 B 1 HETATM 14 O O2P PLP . . . H 4 30.888 5.561 15.873 1 69.69 ? O2P PLP 1002 B 1 HETATM 15 O O3P PLP . . . H 4 28.544 5.944 16.781 1 68.37 ? O3P PLP 1002 B 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 37 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 15 #