data_8GKU # _model_server_result.job_id gxTVR6Gy-n5z1gF744ENDA _model_server_result.datetime_utc '2024-10-10 11:27:01' _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 8gku # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":601}' # _entry.id 8GKU # _exptl.entry_id 8GKU _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 90 _cell.angle_gamma 120 _cell.entry_id 8GKU _cell.length_a 158.324 _cell.length_b 158.324 _cell.length_c 207.65 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GKU _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2 # 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' 12_564 x,x-y+1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -79.162 137.112606 -34.608333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 F 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 covale ? covale1 A NZ LYS 269 A LYS 280 1_555 E C4A PLP . A PLP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale2 B NZ LYS 269 B LYS 280 1_555 F C4A PLP . B PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _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 8GKU _atom_sites.fract_transf_matrix[1][1] 0.006316 _atom_sites.fract_transf_matrix[1][2] 0.003647 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007293 _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] 0.004816 _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 ZV1 A 1 601 601 ZV1 355 . D 3 GLY A 1 602 701 GLY GLY . E 4 PLP A 1 603 280 PLP LLP . F 4 PLP B 1 601 280 PLP LLP . G 5 HOH A 1 701 14 HOH HOH . G 5 HOH A 2 702 19 HOH HOH . G 5 HOH A 3 703 7 HOH HOH . G 5 HOH A 4 704 46 HOH HOH . G 5 HOH A 5 705 39 HOH HOH . G 5 HOH A 6 706 58 HOH HOH . G 5 HOH A 7 707 12 HOH HOH . G 5 HOH A 8 708 59 HOH HOH . G 5 HOH A 9 709 53 HOH HOH . G 5 HOH A 10 710 8 HOH HOH . G 5 HOH A 11 711 63 HOH HOH . G 5 HOH A 12 712 70 HOH HOH . G 5 HOH A 13 713 13 HOH HOH . G 5 HOH A 14 714 3 HOH HOH . G 5 HOH A 15 715 32 HOH HOH . G 5 HOH A 16 716 62 HOH HOH . G 5 HOH A 17 717 49 HOH HOH . G 5 HOH A 18 718 9 HOH HOH . G 5 HOH A 19 719 29 HOH HOH . G 5 HOH A 20 720 31 HOH HOH . G 5 HOH A 21 721 4 HOH HOH . G 5 HOH A 22 722 41 HOH HOH . G 5 HOH A 23 723 61 HOH HOH . G 5 HOH A 24 724 2 HOH HOH . G 5 HOH A 25 725 43 HOH HOH . G 5 HOH A 26 726 68 HOH HOH . G 5 HOH A 27 727 35 HOH HOH . G 5 HOH A 28 728 34 HOH HOH . G 5 HOH A 29 729 66 HOH HOH . G 5 HOH A 30 730 37 HOH HOH . G 5 HOH A 31 731 26 HOH HOH . G 5 HOH A 32 732 30 HOH HOH . G 5 HOH A 33 733 48 HOH HOH . G 5 HOH A 34 734 50 HOH HOH . G 5 HOH A 35 735 15 HOH HOH . G 5 HOH A 36 736 52 HOH HOH . G 5 HOH A 37 737 56 HOH HOH . G 5 HOH A 38 738 47 HOH HOH . G 5 HOH A 39 739 18 HOH HOH . G 5 HOH A 40 740 28 HOH HOH . G 5 HOH A 41 741 55 HOH HOH . G 5 HOH A 42 742 64 HOH HOH . G 5 HOH A 43 743 16 HOH HOH . H 5 HOH B 1 701 45 HOH HOH . H 5 HOH B 2 702 22 HOH HOH . H 5 HOH B 3 703 21 HOH HOH . H 5 HOH B 4 704 25 HOH HOH . H 5 HOH B 5 705 20 HOH HOH . H 5 HOH B 6 706 57 HOH HOH . H 5 HOH B 7 707 10 HOH HOH . H 5 HOH B 8 708 27 HOH HOH . H 5 HOH B 9 709 65 HOH HOH . H 5 HOH B 10 710 5 HOH HOH . H 5 HOH B 11 711 23 HOH HOH . H 5 HOH B 12 712 69 HOH HOH . H 5 HOH B 13 713 1 HOH HOH . H 5 HOH B 14 714 11 HOH HOH . H 5 HOH B 15 715 60 HOH HOH . H 5 HOH B 16 716 40 HOH HOH . H 5 HOH B 17 717 17 HOH HOH . H 5 HOH B 18 718 54 HOH HOH . H 5 HOH B 19 719 67 HOH HOH . H 5 HOH B 20 720 36 HOH HOH . H 5 HOH B 21 721 24 HOH HOH . H 5 HOH B 22 722 51 HOH HOH . H 5 HOH B 23 723 44 HOH HOH . H 5 HOH B 24 724 33 HOH HOH . H 5 HOH B 25 725 42 HOH HOH . H 5 HOH B 26 726 38 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 4 -9.248 75.009 2.257 1 65.26 ? N1 PLP 601 B 1 HETATM 2 C C2 PLP . . . F 4 -7.967 75.101 2.617 1 57.9 ? C2 PLP 601 B 1 HETATM 3 C C2A PLP . . . F 4 -7.231 76.473 2.563 1 59.88 ? C2A PLP 601 B 1 HETATM 4 C C3 PLP . . . F 4 -7.267 73.944 3.049 1 73.42 ? C3 PLP 601 B 1 HETATM 5 O O3 PLP . . . F 4 -5.924 74.051 3.425 1 86.26 ? O3 PLP 601 B 1 HETATM 6 C C4 PLP . . . F 4 -7.891 72.72 3.107 1 75.01 ? C4 PLP 601 B 1 HETATM 7 C C4A PLP . . . F 4 -7.015 71.459 3.612 1 70.4 ? C4A PLP 601 B 1 HETATM 8 C C5 PLP . . . F 4 -9.207 72.616 2.746 1 83.05 ? C5 PLP 601 B 1 HETATM 9 C C6 PLP . . . F 4 -9.892 73.764 2.312 1 76.95 ? C6 PLP 601 B 1 HETATM 10 C C5A PLP . . . F 4 -10.004 71.27 2.751 1 86.67 ? C5A PLP 601 B 1 HETATM 11 O O4P PLP . . . F 4 -9.944 70.512 3.938 1 83.16 ? O4P PLP 601 B 1 HETATM 12 P P PLP . . . F 4 -10.725 69.177 3.908 1 63.91 ? P PLP 601 B 1 HETATM 13 O O1P PLP . . . F 4 -9.946 68.162 3.144 1 76.32 ? O1P PLP 601 B 1 HETATM 14 O O2P PLP . . . F 4 -10.954 68.687 5.282 1 65.9 ? O2P PLP 601 B 1 HETATM 15 O O3P PLP . . . F 4 -12.073 69.403 3.209 1 65 ? O3P PLP 601 B 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #