data_7NWE # _model_server_result.job_id XVNMyWPlVAO_F0QSyIwaFA _model_server_result.datetime_utc '2024-11-14 03:48:26' _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 7nwe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 7NWE # _exptl.entry_id 7NWE _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 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 90 _cell.entry_id 7NWE _cell.length_a 66.49 _cell.length_b 103.461 _cell.length_c 107.749 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7NWE _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 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 disulf ? disulf1 A SG CYS 338 A CYS 335 1_555 A SG CYS 341 A CYS 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 B SG CYS 338 B CYS 335 1_555 B SG CYS 341 B CYS 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? covale ? covale1 A NZ LYS 225 A LYS 222 1_555 D C4A PLP . A PLP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.269 ? covale ? covale2 B NZ LYS 225 B LYS 222 1_555 F C4A PLP . B PLP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.273 ? metalc ? metalc1 B OD2 ASP 136 B ASP 133 1_555 G MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc2 G MG MG . B MG 403 1_555 I O HOH . B HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc3 G MG MG . B MG 403 1_555 I O HOH . B HOH 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc4 G MG MG . B MG 403 1_555 I O HOH . B HOH 513 4_455 ? ? ? ? ? ? ? ? ? ? ? ? 1.844 ? # _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 7NWE _atom_sites.fract_transf_matrix[1][1] 0.01504 _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] 0.009665 _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] 0.009281 _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 UTE A 1 401 401 UTE LIG . D 3 PLP A 1 402 420 PLP PLP . E 2 UTE B 1 401 401 UTE LIG . F 3 PLP B 1 402 420 PLP PLP . G 4 MG B 1 403 430 MG MG . H 5 HOH A 1 501 21 HOH HOH . H 5 HOH A 2 502 45 HOH HOH . H 5 HOH A 3 503 20 HOH HOH . H 5 HOH A 4 504 63 HOH HOH . H 5 HOH A 5 505 44 HOH HOH . H 5 HOH A 6 506 4 HOH HOH . H 5 HOH A 7 507 65 HOH HOH . H 5 HOH A 8 508 41 HOH HOH . H 5 HOH A 9 509 31 HOH HOH . H 5 HOH A 10 510 29 HOH HOH . H 5 HOH A 11 511 12 HOH HOH . H 5 HOH A 12 512 6 HOH HOH . H 5 HOH A 13 513 38 HOH HOH . H 5 HOH A 14 514 25 HOH HOH . H 5 HOH A 15 515 54 HOH HOH . H 5 HOH A 16 516 39 HOH HOH . H 5 HOH A 17 517 2 HOH HOH . H 5 HOH A 18 518 15 HOH HOH . H 5 HOH A 19 519 47 HOH HOH . H 5 HOH A 20 520 48 HOH HOH . H 5 HOH A 21 521 5 HOH HOH . H 5 HOH A 22 522 43 HOH HOH . H 5 HOH A 23 523 30 HOH HOH . H 5 HOH A 24 524 23 HOH HOH . H 5 HOH A 25 525 32 HOH HOH . H 5 HOH A 26 526 33 HOH HOH . H 5 HOH A 27 527 1 HOH HOH . H 5 HOH A 28 528 24 HOH HOH . H 5 HOH A 29 529 60 HOH HOH . H 5 HOH A 30 530 40 HOH HOH . H 5 HOH A 31 531 62 HOH HOH . H 5 HOH A 32 532 58 HOH HOH . H 5 HOH A 33 533 14 HOH HOH . I 5 HOH B 1 501 61 HOH HOH . I 5 HOH B 2 502 22 HOH HOH . I 5 HOH B 3 503 53 HOH HOH . I 5 HOH B 4 504 35 HOH HOH . I 5 HOH B 5 505 51 HOH HOH . I 5 HOH B 6 506 37 HOH HOH . I 5 HOH B 7 507 57 HOH HOH . I 5 HOH B 8 508 27 HOH HOH . I 5 HOH B 9 509 46 HOH HOH . I 5 HOH B 10 510 66 HOH HOH . I 5 HOH B 11 511 49 HOH HOH . I 5 HOH B 12 512 9 HOH HOH . I 5 HOH B 13 513 67 HOH HOH . I 5 HOH B 14 514 64 HOH HOH . I 5 HOH B 15 515 55 HOH HOH . I 5 HOH B 16 516 17 HOH HOH . I 5 HOH B 17 517 28 HOH HOH . I 5 HOH B 18 518 19 HOH HOH . I 5 HOH B 19 519 42 HOH HOH . I 5 HOH B 20 520 13 HOH HOH . I 5 HOH B 21 521 10 HOH HOH . I 5 HOH B 22 522 7 HOH HOH . I 5 HOH B 23 523 26 HOH HOH . I 5 HOH B 24 524 16 HOH HOH . I 5 HOH B 25 525 52 HOH HOH . I 5 HOH B 26 526 11 HOH HOH . I 5 HOH B 27 527 18 HOH HOH . I 5 HOH B 28 528 59 HOH HOH . I 5 HOH B 29 529 36 HOH HOH . I 5 HOH B 30 530 3 HOH HOH . I 5 HOH B 31 531 56 HOH HOH . I 5 HOH B 32 532 8 HOH HOH . I 5 HOH B 33 533 50 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 . . . D 3 -36.141 -1.393 -19.822 1 53.95 ? N1 PLP 402 A 1 HETATM 2 C C2 PLP . . . D 3 -35.212 -1.467 -18.872 1 57.69 ? C2 PLP 402 A 1 HETATM 3 C C2A PLP . . . D 3 -34.379 -0.258 -18.591 1 59.72 ? C2A PLP 402 A 1 HETATM 4 C C3 PLP . . . D 3 -35.028 -2.658 -18.148 1 60.56 ? C3 PLP 402 A 1 HETATM 5 O O3 PLP . . . D 3 -34.075 -2.692 -17.187 1 57.75 ? O3 PLP 402 A 1 HETATM 6 C C4 PLP . . . D 3 -35.829 -3.781 -18.439 1 63.52 ? C4 PLP 402 A 1 HETATM 7 C C4A PLP . . . D 3 -35.625 -5.019 -17.68 1 59.36 ? C4A PLP 402 A 1 HETATM 8 C C5 PLP . . . D 3 -36.793 -3.668 -19.457 1 60.26 ? C5 PLP 402 A 1 HETATM 9 C C6 PLP . . . D 3 -36.909 -2.467 -20.104 1 55.96 ? C6 PLP 402 A 1 HETATM 10 C C5A PLP . . . D 3 -37.71 -4.8 -19.83 1 60.11 ? C5A PLP 402 A 1 HETATM 11 O O4P PLP . . . D 3 -36.981 -5.988 -20.269 1 63.86 ? O4P PLP 402 A 1 HETATM 12 P P PLP . . . D 3 -37.702 -7.436 -20.267 1 64.98 ? P PLP 402 A 1 HETATM 13 O O1P PLP . . . D 3 -38.781 -7.375 -21.334 1 59.02 ? O1P PLP 402 A 1 HETATM 14 O O2P PLP . . . D 3 -38.267 -7.61 -18.867 1 69.17 ? O2P PLP 402 A 1 HETATM 15 O O3P PLP . . . D 3 -36.607 -8.438 -20.595 1 62.89 ? O3P PLP 402 A 1 # _model_server_stats.io_time_ms 198 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 15 #