data_2EGY # _model_server_result.job_id xV3cRNQViuZ80mgV4fEqLA _model_server_result.datetime_utc '2024-12-19 13:38:22' _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 2egy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":400}' # _entry.id 2EGY # _exptl.entry_id 2EGY _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 100.21 _cell.angle_gamma 90 _cell.entry_id 2EGY _cell.length_a 56.415 _cell.length_b 138.51 _cell.length_c 111.745 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2EGY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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,PQS dimeric 2 author_and_software_defined_assembly 1 PISA,PQS 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,K,L 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 # 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 238 A LYS 238 1_555 E C4A PLP . A PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.28 ? covale ? covale2 B NZ LYS 238 B LYS 238 1_555 F C4A PLP . B PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.28 ? covale ? covale3 C NZ LYS 238 C LYS 238 1_555 G C4A PLP . C PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.288 ? covale ? covale4 D NZ LYS 238 D LYS 238 1_555 H C4A PLP . D PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.296 ? # _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 247 n y N1 C6 PLP sing 248 n y C2 C2A PLP sing 249 n n C2 C3 PLP sing 250 n y C2A H2A1 PLP sing 251 n n C2A H2A2 PLP sing 252 n n C2A H2A3 PLP sing 253 n n C3 O3 PLP sing 254 n n C3 C4 PLP doub 255 n y O3 HO3 PLP sing 256 n n C4 C4A PLP sing 257 n n C4 C5 PLP sing 258 n y C4A O4A PLP doub 259 n n C4A H4A PLP sing 260 n n C5 C6 PLP doub 261 n y C5 C5A PLP sing 262 n n C6 H6 PLP sing 263 n n C5A O4P PLP sing 264 n n C5A H5A1 PLP sing 265 n n C5A H5A2 PLP sing 266 n n O4P P PLP sing 267 n n P O1P PLP doub 268 n n P O2P PLP sing 269 n n P O3P PLP sing 270 n n O2P HOP2 PLP sing 271 n n O3P HOP3 PLP sing 272 n n # _atom_sites.entry_id 2EGY _atom_sites.fract_transf_matrix[1][1] 0.017726 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003194 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00722 _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] 0.009093 _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 1 400 400 PLP PLP . F 2 PLP B 1 400 400 PLP PLP . G 2 PLP C 1 400 400 PLP PLP . H 2 PLP D 1 400 400 PLP PLP . I 3 HOH A 1 401 9 HOH HOH . I 3 HOH A 2 402 11 HOH HOH . I 3 HOH A 3 403 19 HOH HOH . I 3 HOH A 4 404 20 HOH HOH . I 3 HOH A 5 405 23 HOH HOH . I 3 HOH A 6 406 26 HOH HOH . I 3 HOH A 7 407 27 HOH HOH . I 3 HOH A 8 408 28 HOH HOH . I 3 HOH A 9 409 30 HOH HOH . I 3 HOH A 10 410 35 HOH HOH . I 3 HOH A 11 411 36 HOH HOH . I 3 HOH A 12 412 38 HOH HOH . I 3 HOH A 13 413 44 HOH HOH . I 3 HOH A 14 414 51 HOH HOH . I 3 HOH A 15 415 55 HOH HOH . I 3 HOH A 16 416 56 HOH HOH . I 3 HOH A 17 417 57 HOH HOH . I 3 HOH A 18 418 64 HOH HOH . I 3 HOH A 19 419 67 HOH HOH . I 3 HOH A 20 420 73 HOH HOH . I 3 HOH A 21 421 75 HOH HOH . I 3 HOH A 22 422 78 HOH HOH . I 3 HOH A 23 423 84 HOH HOH . J 3 HOH B 1 401 3 HOH HOH . J 3 HOH B 2 402 5 HOH HOH . J 3 HOH B 3 403 6 HOH HOH . J 3 HOH B 4 404 10 HOH HOH . J 3 HOH B 5 405 15 HOH HOH . J 3 HOH B 6 406 17 HOH HOH . J 3 HOH B 7 407 22 HOH HOH . J 3 HOH B 8 408 25 HOH HOH . J 3 HOH B 9 409 29 HOH HOH . J 3 HOH B 10 410 39 HOH HOH . J 3 HOH B 11 411 43 HOH HOH . J 3 HOH B 12 412 46 HOH HOH . J 3 HOH B 13 413 47 HOH HOH . J 3 HOH B 14 414 48 HOH HOH . J 3 HOH B 15 415 69 HOH HOH . J 3 HOH B 16 416 70 HOH HOH . J 3 HOH B 17 417 71 HOH HOH . J 3 HOH B 18 418 77 HOH HOH . J 3 HOH B 19 419 80 HOH HOH . J 3 HOH B 20 420 82 HOH HOH . J 3 HOH B 21 421 83 HOH HOH . K 3 HOH C 1 401 7 HOH HOH . K 3 HOH C 2 402 13 HOH HOH . K 3 HOH C 3 403 14 HOH HOH . K 3 HOH C 4 404 16 HOH HOH . K 3 HOH C 5 405 18 HOH HOH . K 3 HOH C 6 406 21 HOH HOH . K 3 HOH C 7 407 24 HOH HOH . K 3 HOH C 8 408 41 HOH HOH . K 3 HOH C 9 409 49 HOH HOH . K 3 HOH C 10 410 53 HOH HOH . K 3 HOH C 11 411 59 HOH HOH . K 3 HOH C 12 412 61 HOH HOH . K 3 HOH C 13 413 62 HOH HOH . K 3 HOH C 14 414 72 HOH HOH . K 3 HOH C 15 415 79 HOH HOH . K 3 HOH C 16 416 81 HOH HOH . L 3 HOH D 1 401 1 HOH HOH . L 3 HOH D 2 402 2 HOH HOH . L 3 HOH D 3 403 4 HOH HOH . L 3 HOH D 4 404 8 HOH HOH . L 3 HOH D 5 405 12 HOH HOH . L 3 HOH D 6 406 31 HOH HOH . L 3 HOH D 7 407 32 HOH HOH . L 3 HOH D 8 408 34 HOH HOH . L 3 HOH D 9 409 37 HOH HOH . L 3 HOH D 10 410 40 HOH HOH . L 3 HOH D 11 411 42 HOH HOH . L 3 HOH D 12 412 45 HOH HOH . L 3 HOH D 13 413 50 HOH HOH . L 3 HOH D 14 414 52 HOH HOH . L 3 HOH D 15 415 54 HOH HOH . L 3 HOH D 16 416 58 HOH HOH . L 3 HOH D 17 417 60 HOH HOH . L 3 HOH D 18 418 63 HOH HOH . L 3 HOH D 19 419 65 HOH HOH . L 3 HOH D 20 420 66 HOH HOH . L 3 HOH D 21 421 68 HOH HOH . L 3 HOH D 22 422 74 HOH HOH . L 3 HOH D 23 423 76 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 . . . G 2 12.32 29.247 48.969 1 46.07 ? N1 PLP 400 C 1 HETATM 2 C C2 PLP . . . G 2 13.062 30.036 48.095 1 42.74 ? C2 PLP 400 C 1 HETATM 3 C C2A PLP . . . G 2 12.604 31.361 47.771 1 42.79 ? C2A PLP 400 C 1 HETATM 4 C C3 PLP . . . G 2 14.313 29.551 47.57 1 45.69 ? C3 PLP 400 C 1 HETATM 5 O O3 PLP . . . G 2 15.055 30.356 46.693 1 40.05 ? O3 PLP 400 C 1 HETATM 6 C C4 PLP . . . G 2 14.782 28.283 47.954 1 45.1 ? C4 PLP 400 C 1 HETATM 7 C C4A PLP . . . G 2 16.051 27.758 47.377 1 50.39 ? C4A PLP 400 C 1 HETATM 8 C C5 PLP . . . G 2 14.033 27.494 48.859 1 47.05 ? C5 PLP 400 C 1 HETATM 9 C C6 PLP . . . G 2 12.779 27.99 49.363 1 45.01 ? C6 PLP 400 C 1 HETATM 10 C C5A PLP . . . G 2 14.57 26.155 49.383 1 47.86 ? C5A PLP 400 C 1 HETATM 11 O O4P PLP . . . G 2 13.661 25.092 49.082 1 42.96 ? O4P PLP 400 C 1 HETATM 12 P P PLP . . . G 2 13.889 23.763 49.652 1 40.91 ? P PLP 400 C 1 HETATM 13 O O1P PLP . . . G 2 15.231 23.173 49.099 1 34.57 ? O1P PLP 400 C 1 HETATM 14 O O2P PLP . . . G 2 13.956 23.867 51.263 1 41.65 ? O2P PLP 400 C 1 HETATM 15 O O3P PLP . . . G 2 12.701 22.811 49.239 1 50.59 ? O3P PLP 400 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 15 #