data_8B06 # _model_server_result.job_id RPOUtkqDMrZH4yy-go0m2g _model_server_result.datetime_utc '2024-10-19 10:28:52' _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 8b06 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 8B06 # _exptl.entry_id 8B06 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.68 _cell.angle_gamma 90 _cell.entry_id 8B06 _cell.length_a 181.789 _cell.length_b 59.048 _cell.length_c 67.092 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8B06 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 B NZ LYS 87 B LYS 87 1_555 C C4A PLP . B PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? metalc ? metalc1 B O GLY 232 B GLY 232 1_555 D CS CS . B CS 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.99 ? metalc ? metalc2 B O GLY 268 B GLY 268 1_555 D CS CS . B CS 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc3 B O PHE 306 B PHE 306 1_555 D CS CS . B CS 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? metalc ? metalc4 B O SER 308 B SER 308 1_555 D CS CS . B CS 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.401 ? metalc ? metalc5 D CS CS . B CS 502 1_555 I O HOH . B HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.976 ? # _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 8B06 _atom_sites.fract_transf_matrix[1][1] 0.005501 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000451 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016935 _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] 0.014955 _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 3 PLP B 1 501 501 PLP PLP . D 4 CS B 1 502 601 CS CS . E 5 SER B 1 503 701 SER SER . F 6 CL B 1 504 1 CL CL . G 6 CL B 1 505 2 CL CL . H 7 HOH A 1 301 25 HOH HOH . H 7 HOH A 2 302 27 HOH HOH . H 7 HOH A 3 303 24 HOH HOH . H 7 HOH A 4 304 31 HOH HOH . H 7 HOH A 5 305 21 HOH HOH . H 7 HOH A 6 306 29 HOH HOH . H 7 HOH A 7 307 47 HOH HOH . H 7 HOH A 8 308 28 HOH HOH . H 7 HOH A 9 309 26 HOH HOH . H 7 HOH A 10 310 32 HOH HOH . H 7 HOH A 11 311 20 HOH HOH . I 7 HOH B 1 601 50 HOH HOH . I 7 HOH B 2 602 39 HOH HOH . I 7 HOH B 3 603 49 HOH HOH . I 7 HOH B 4 604 15 HOH HOH . I 7 HOH B 5 605 16 HOH HOH . I 7 HOH B 6 606 11 HOH HOH . I 7 HOH B 7 607 19 HOH HOH . I 7 HOH B 8 608 41 HOH HOH . I 7 HOH B 9 609 8 HOH HOH . I 7 HOH B 10 610 23 HOH HOH . I 7 HOH B 11 611 10 HOH HOH . I 7 HOH B 12 612 18 HOH HOH . I 7 HOH B 13 613 1 HOH HOH . I 7 HOH B 14 614 55 HOH HOH . I 7 HOH B 15 615 5 HOH HOH . I 7 HOH B 16 616 17 HOH HOH . I 7 HOH B 17 617 4 HOH HOH . I 7 HOH B 18 618 30 HOH HOH . I 7 HOH B 19 619 56 HOH HOH . I 7 HOH B 20 620 9 HOH HOH . I 7 HOH B 21 621 13 HOH HOH . I 7 HOH B 22 622 46 HOH HOH . I 7 HOH B 23 623 40 HOH HOH . I 7 HOH B 24 624 33 HOH HOH . I 7 HOH B 25 625 7 HOH HOH . I 7 HOH B 26 626 37 HOH HOH . I 7 HOH B 27 627 53 HOH HOH . I 7 HOH B 28 628 35 HOH HOH . I 7 HOH B 29 629 6 HOH HOH . I 7 HOH B 30 630 22 HOH HOH . I 7 HOH B 31 631 34 HOH HOH . I 7 HOH B 32 632 42 HOH HOH . I 7 HOH B 33 633 3 HOH HOH . I 7 HOH B 34 634 52 HOH HOH . I 7 HOH B 35 635 44 HOH HOH . I 7 HOH B 36 636 36 HOH HOH . I 7 HOH B 37 637 2 HOH HOH . I 7 HOH B 38 638 38 HOH HOH . I 7 HOH B 39 639 43 HOH HOH . I 7 HOH B 40 640 57 HOH HOH . I 7 HOH B 41 641 51 HOH HOH . I 7 HOH B 42 642 54 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 . . . C 3 84.037 13.812 11.846 1 44.06 ? N1 PLP 501 B 1 HETATM 2 C C2 PLP . . . C 3 83.947 14.459 10.63 1 44.47 ? C2 PLP 501 B 1 HETATM 3 C C2A PLP . . . C 3 85.092 14.426 9.658 1 44.53 ? C2A PLP 501 B 1 HETATM 4 C C3 PLP . . . C 3 82.781 15.149 10.301 1 44.98 ? C3 PLP 501 B 1 HETATM 5 O O3 PLP . . . C 3 82.674 15.789 9.093 1 46.15 ? O3 PLP 501 B 1 HETATM 6 C C4 PLP . . . C 3 81.692 15.192 11.167 1 44.88 ? C4 PLP 501 B 1 HETATM 7 C C4A PLP . . . C 3 80.352 15.234 10.489 1 45.17 ? C4A PLP 501 B 1 HETATM 8 C C5 PLP . . . C 3 81.812 14.549 12.399 1 44.09 ? C5 PLP 501 B 1 HETATM 9 C C6 PLP . . . C 3 82.975 13.856 12.725 1 43.96 ? C6 PLP 501 B 1 HETATM 10 C C5A PLP . . . C 3 80.663 14.572 13.378 1 43.82 ? C5A PLP 501 B 1 HETATM 11 O O4P PLP . . . C 3 79.771 13.582 12.936 1 43.21 ? O4P PLP 501 B 1 HETATM 12 P P PLP . . . C 3 79.117 12.509 13.925 1 42.85 ? P PLP 501 B 1 HETATM 13 O O1P PLP . . . C 3 79.669 11.141 13.597 1 42.46 ? O1P PLP 501 B 1 HETATM 14 O O2P PLP . . . C 3 79.418 12.86 15.362 1 42.97 -1 O2P PLP 501 B 1 HETATM 15 O O3P PLP . . . C 3 77.624 12.522 13.702 1 43.4 ? O3P PLP 501 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #