data_8VHH # _model_server_result.job_id 1CDXJQxXfud5UfGaBNwYFw _model_server_result.datetime_utc '2024-12-02 06:05:52' _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 8vhh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8VHH # _exptl.entry_id 8VHH _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 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 8VHH _cell.length_a 165.698 _cell.length_b 165.698 _cell.length_c 83.061 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VHH _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall 'I 4' _symmetry.space_group_name_H-M 'I 4' # _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,J,K _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 ? 2 C N N ? 2 G 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 metalc ? metalc1 A OG SER 228 A SER 228 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.284 ? metalc ? metalc2 A O ALA 263 A ALA 263 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? metalc ? metalc3 A OG SER 265 A SER 265 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc4 A O TYR 301 A TYR 301 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? metalc ? metalc5 A O GLY 303 A GLY 303 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc6 D K K . A K 402 1_555 J O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc7 B O ALA 263 B ALA 263 1_555 H K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? metalc ? metalc8 B OG SER 265 B SER 265 1_555 H K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.757 ? metalc ? metalc9 B O TYR 301 B TYR 301 1_555 H K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc10 B O GLY 303 B GLY 303 1_555 H K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? metalc ? metalc11 H K K . B K 402 1_555 K O HOH . B HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? # _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 8VHH _atom_sites.fract_transf_matrix[1][1] 0.006035 _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] 0.006035 _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] 0.012039 _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 PLP A 1 401 401 PLP PLP . D 3 K A 1 402 1 K K . E 4 PO4 A 1 403 1 PO4 PO4 . F 4 PO4 A 1 404 3 PO4 PO4 . G 2 PLP B 1 401 401 PLP PLP . H 3 K B 1 402 2 K K . I 4 PO4 B 1 403 2 PO4 PO4 . J 5 HOH A 1 501 1 HOH HOH . J 5 HOH A 2 502 48 HOH HOH . J 5 HOH A 3 503 16 HOH HOH . J 5 HOH A 4 504 40 HOH HOH . J 5 HOH A 5 505 57 HOH HOH . J 5 HOH A 6 506 73 HOH HOH . J 5 HOH A 7 507 41 HOH HOH . J 5 HOH A 8 508 8 HOH HOH . J 5 HOH A 9 509 77 HOH HOH . J 5 HOH A 10 510 23 HOH HOH . J 5 HOH A 11 511 19 HOH HOH . J 5 HOH A 12 512 32 HOH HOH . J 5 HOH A 13 513 45 HOH HOH . J 5 HOH A 14 514 11 HOH HOH . J 5 HOH A 15 515 62 HOH HOH . J 5 HOH A 16 516 91 HOH HOH . J 5 HOH A 17 517 81 HOH HOH . J 5 HOH A 18 518 22 HOH HOH . J 5 HOH A 19 519 12 HOH HOH . J 5 HOH A 20 520 54 HOH HOH . J 5 HOH A 21 521 34 HOH HOH . J 5 HOH A 22 522 68 HOH HOH . J 5 HOH A 23 523 26 HOH HOH . J 5 HOH A 24 524 88 HOH HOH . J 5 HOH A 25 525 89 HOH HOH . J 5 HOH A 26 526 37 HOH HOH . J 5 HOH A 27 527 79 HOH HOH . J 5 HOH A 28 528 86 HOH HOH . J 5 HOH A 29 529 39 HOH HOH . J 5 HOH A 30 530 35 HOH HOH . J 5 HOH A 31 531 53 HOH HOH . J 5 HOH A 32 532 13 HOH HOH . J 5 HOH A 33 533 61 HOH HOH . J 5 HOH A 34 534 85 HOH HOH . J 5 HOH A 35 535 47 HOH HOH . J 5 HOH A 36 536 43 HOH HOH . J 5 HOH A 37 537 67 HOH HOH . J 5 HOH A 38 538 29 HOH HOH . J 5 HOH A 39 539 4 HOH HOH . J 5 HOH A 40 540 25 HOH HOH . J 5 HOH A 41 541 80 HOH HOH . J 5 HOH A 42 542 82 HOH HOH . J 5 HOH A 43 543 14 HOH HOH . J 5 HOH A 44 544 38 HOH HOH . J 5 HOH A 45 545 60 HOH HOH . J 5 HOH A 46 546 15 HOH HOH . J 5 HOH A 47 547 51 HOH HOH . J 5 HOH A 48 548 56 HOH HOH . J 5 HOH A 49 549 7 HOH HOH . J 5 HOH A 50 550 28 HOH HOH . J 5 HOH A 51 551 75 HOH HOH . J 5 HOH A 52 552 74 HOH HOH . J 5 HOH A 53 553 55 HOH HOH . J 5 HOH A 54 554 6 HOH HOH . J 5 HOH A 55 555 17 HOH HOH . J 5 HOH A 56 556 65 HOH HOH . J 5 HOH A 57 557 87 HOH HOH . J 5 HOH A 58 558 9 HOH HOH . J 5 HOH A 59 559 63 HOH HOH . J 5 HOH A 60 560 46 HOH HOH . J 5 HOH A 61 561 94 HOH HOH . J 5 HOH A 62 562 58 HOH HOH . J 5 HOH A 63 563 70 HOH HOH . J 5 HOH A 64 564 93 HOH HOH . J 5 HOH A 65 565 64 HOH HOH . K 5 HOH B 1 501 42 HOH HOH . K 5 HOH B 2 502 92 HOH HOH . K 5 HOH B 3 503 2 HOH HOH . K 5 HOH B 4 504 27 HOH HOH . K 5 HOH B 5 505 84 HOH HOH . K 5 HOH B 6 506 24 HOH HOH . K 5 HOH B 7 507 36 HOH HOH . K 5 HOH B 8 508 10 HOH HOH . K 5 HOH B 9 509 59 HOH HOH . K 5 HOH B 10 510 3 HOH HOH . K 5 HOH B 11 511 72 HOH HOH . K 5 HOH B 12 512 66 HOH HOH . K 5 HOH B 13 513 33 HOH HOH . K 5 HOH B 14 514 78 HOH HOH . K 5 HOH B 15 515 21 HOH HOH . K 5 HOH B 16 516 18 HOH HOH . K 5 HOH B 17 517 30 HOH HOH . K 5 HOH B 18 518 31 HOH HOH . K 5 HOH B 19 519 76 HOH HOH . K 5 HOH B 20 520 49 HOH HOH . K 5 HOH B 21 521 20 HOH HOH . K 5 HOH B 22 522 50 HOH HOH . K 5 HOH B 23 523 5 HOH HOH . K 5 HOH B 24 524 44 HOH HOH . K 5 HOH B 25 525 83 HOH HOH . K 5 HOH B 26 526 71 HOH HOH . K 5 HOH B 27 527 52 HOH HOH . K 5 HOH B 28 528 69 HOH HOH . K 5 HOH B 29 529 90 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 2 24.102 45.388 -0.691 1 50.2 ? N1 PLP 401 A 1 HETATM 2 C C2 PLP . . . C 2 23.355 44.697 -1.62 1 51.61 ? C2 PLP 401 A 1 HETATM 3 C C2A PLP . . . C 2 21.896 44.991 -1.784 1 40.4 ? C2A PLP 401 A 1 HETATM 4 C C3 PLP . . . C 2 23.954 43.724 -2.41 1 51.63 ? C3 PLP 401 A 1 HETATM 5 O O3 PLP . . . C 2 23.202 43.041 -3.33 1 61.97 ? O3 PLP 401 A 1 HETATM 6 C C4 PLP . . . C 2 25.306 43.43 -2.277 1 53.09 ? C4 PLP 401 A 1 HETATM 7 C C4A PLP . . . C 2 25.798 42.237 -3.055 1 56.36 ? C4A PLP 401 A 1 HETATM 8 O O4A PLP . . . C 2 26.921 41.745 -2.971 1 61.42 ? O4A PLP 401 A 1 HETATM 9 C C5 PLP . . . C 2 26.06 44.133 -1.326 1 51.02 ? C5 PLP 401 A 1 HETATM 10 C C6 PLP . . . C 2 25.446 45.111 -0.549 1 49.2 ? C6 PLP 401 A 1 HETATM 11 C C5A PLP . . . C 2 27.536 43.91 -1.093 1 58.25 ? C5A PLP 401 A 1 HETATM 12 O O4P PLP . . . C 2 28.255 44.112 -2.289 1 51.42 ? O4P PLP 401 A 1 HETATM 13 P P PLP . . . C 2 29.553 45.05 -2.216 1 45.64 ? P PLP 401 A 1 HETATM 14 O O1P PLP . . . C 2 30.272 45.076 -3.544 1 43.13 ? O1P PLP 401 A 1 HETATM 15 O O2P PLP . . . C 2 30.463 44.494 -1.148 1 44.53 ? O2P PLP 401 A 1 HETATM 16 O O3P PLP . . . C 2 29.116 46.443 -1.83 1 38.41 ? O3P PLP 401 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 371 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 16 #