data_6SNL # _model_server_result.job_id spyin3Br3JDB8snAPqdMUQ _model_server_result.datetime_utc '2024-11-28 18:09:26' _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 6snl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 6SNL # _exptl.entry_id 6SNL _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 6 _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 6SNL _cell.length_a 115.113 _cell.length_b 301.521 _cell.length_c 140.657 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6SNL _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G,H,N,R 1 1 B,I,J,S 2 1 E,O,U 2 2 C,F,K,L,M,P,Q,T,V 3 1 # 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_445 -x-1/2,-y-1/2,z+1/2 -1 0 0 0 -1 0 0 0 1 -57.5565 -150.7605 70.3285 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 I N N ? 2 K N N ? 2 N N N ? 2 O N N ? 2 P 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 179 A LYS 179 1_555 G C4A PLP . A PLP 401 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.429 ? covale ? covale2 B NZ LYS 179 B LYS 179 1_555 I C4A PLP . B PLP 401 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.429 ? covale ? covale3 C NZ LYS 179 C LYS 179 1_555 K C4A PLP . C PLP 401 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.432 ? covale ? covale4 D NZ LYS 179 D LYS 179 1_555 N C4A PLP . D PLP 401 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.431 ? covale ? covale5 E NZ LYS 179 E LYS 179 1_555 O C4A PLP . E PLP 401 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.43 ? covale ? covale6 F NZ LYS 179 F LYS 179 1_555 P C4A PLP . F PLP 401 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.43 ? # _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 317 n y N1 C6 PLP sing 318 n y C2 C2A PLP sing 319 n n C2 C3 PLP sing 320 n y C2A H2A1 PLP sing 321 n n C2A H2A2 PLP sing 322 n n C2A H2A3 PLP sing 323 n n C3 O3 PLP sing 324 n n C3 C4 PLP doub 325 n y O3 HO3 PLP sing 326 n n C4 C4A PLP sing 327 n n C4 C5 PLP sing 328 n y C4A O4A PLP doub 329 n n C4A H4A PLP sing 330 n n C5 C6 PLP doub 331 n y C5 C5A PLP sing 332 n n C6 H6 PLP sing 333 n n C5A O4P PLP sing 334 n n C5A H5A1 PLP sing 335 n n C5A H5A2 PLP sing 336 n n O4P P PLP sing 337 n n P O1P PLP doub 338 n n P O2P PLP sing 339 n n P O3P PLP sing 340 n n O2P HOP2 PLP sing 341 n n O3P HOP3 PLP sing 342 n n # _atom_sites.entry_id 6SNL _atom_sites.fract_transf_matrix[1][1] 0.008687 _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] 0.003317 _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] 0.007109 _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 G 2 PLP A 1 401 1180 PLP PLP . H 3 GOL A 1 402 2 GOL GOL . I 2 PLP B 1 401 1180 PLP PLP . J 3 GOL B 1 402 1 GOL GOL . K 2 PLP C 1 401 1180 PLP PLP . L 4 CL C 1 402 1 CL CL . M 5 P6G C 1 403 1 P6G P6G . N 2 PLP D 1 401 1180 PLP PLP . O 2 PLP E 1 401 1180 PLP PLP . P 2 PLP F 1 401 1180 PLP PLP . Q 4 CL F 1 402 2 CL CL . R 6 HOH A 1 501 11 HOH HOH . R 6 HOH A 2 502 9 HOH HOH . R 6 HOH A 3 503 19 HOH HOH . S 6 HOH B 1 501 17 HOH HOH . T 6 HOH C 1 501 1 HOH HOH . T 6 HOH C 2 502 2 HOH HOH . U 6 HOH E 1 501 18 HOH HOH . U 6 HOH E 2 502 4 HOH HOH . U 6 HOH E 3 503 8 HOH HOH . U 6 HOH E 4 504 16 HOH HOH . V 6 HOH F 1 501 6 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 . B . I 2 -33.586 -54.772 33.215 1 45.36 ? N1 PLP 401 B 1 HETATM 2 C C2 PLP . B . I 2 -33.232 -53.528 32.756 1 44.89 ? C2 PLP 401 B 1 HETATM 3 C C2A PLP . B . I 2 -32.347 -52.736 33.648 1 44.76 ? C2A PLP 401 B 1 HETATM 4 C C3 PLP . B . I 2 -33.666 -53.027 31.534 1 45.18 ? C3 PLP 401 B 1 HETATM 5 O O3 PLP . B . I 2 -33.263 -51.772 31.155 1 44.19 ? O3 PLP 401 B 1 HETATM 6 C C4 PLP . B . I 2 -34.505 -53.805 30.709 1 45.87 ? C4 PLP 401 B 1 HETATM 7 C C4A PLP . B . I 2 -34.983 -53.317 29.41 1 45.28 ? C4A PLP 401 B 1 HETATM 8 C C5 PLP . B . I 2 -34.863 -55.059 31.164 1 45.86 ? C5 PLP 401 B 1 HETATM 9 C C6 PLP . B . I 2 -34.38 -55.502 32.429 1 45.4 ? C6 PLP 401 B 1 HETATM 10 C C5A PLP . B . I 2 -35.756 -55.971 30.379 1 45.29 ? C5A PLP 401 B 1 HETATM 11 O O4P PLP . B . I 2 -36.993 -55.418 30.248 1 45.77 ? O4P PLP 401 B 1 HETATM 12 P P PLP . B . I 2 -38.074 -56.363 29.099 1 46.19 ? P PLP 401 B 1 HETATM 13 O O1P PLP . B . I 2 -37.142 -56.285 27.902 1 46.56 ? O1P PLP 401 B 1 HETATM 14 O O2P PLP . B . I 2 -38.201 -57.694 29.802 1 45.74 ? O2P PLP 401 B 1 HETATM 15 O O3P PLP . B . I 2 -39.257 -55.445 29.081 1 47.04 ? O3P PLP 401 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 67 _model_server_stats.query_time_ms 704 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 15 #