data_6AM9 # _model_server_result.job_id J5BqSSmNr6Eu5FQPXpTT4w _model_server_result.datetime_utc '2024-11-23 21:37:58' _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 6am9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":403}' # _entry.id 6AM9 # _exptl.entry_id 6AM9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 336.235 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE' _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 90 _cell.angle_gamma 90 _cell.entry_id 6AM9 _cell.length_a 87.502 _cell.length_b 109.122 _cell.length_c 160.491 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6AM9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,O,P 1 1 C,D,J,K,L,M,N,Q,R 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id G _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 metalc ? metalc1 A O GLY 48 A GLY 48 1_555 F NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.926 ? metalc ? metalc2 A O SER 263 A SER 263 1_555 E NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc3 A OG SER 263 A SER 263 1_555 E NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.08 ? metalc ? metalc4 A OG SER 265 A SER 265 1_555 E NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? metalc ? metalc5 A O TYR 301 A TYR 301 1_555 E NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? metalc ? metalc6 A O GLY 303 A GLY 303 1_555 E NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc7 E NA NA . A NA 401 1_555 O O HOH . A HOH 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc8 F NA NA . A NA 402 1_555 B O PRO 50 B PRO 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.2 ? metalc ? metalc9 B O SER 263 B SER 263 1_555 I NA NA . B NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc10 B OG SER 265 B SER 265 1_555 I NA NA . B NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc11 B O TYR 301 B TYR 301 1_555 I NA NA . B NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc12 B O GLY 303 B GLY 303 1_555 I NA NA . B NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc13 I NA NA . B NA 402 1_555 P O HOH . B HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc14 C O GLY 48 C GLY 48 1_555 L NA NA . C NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? metalc ? metalc15 C O SER 263 C SER 263 1_555 K NA NA . C NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc16 C OG SER 265 C SER 265 1_555 K NA NA . C NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.786 ? metalc ? metalc17 C O TYR 301 C TYR 301 1_555 K NA NA . C NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc18 C O GLY 303 C GLY 303 1_555 K NA NA . C NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc19 L NA NA . C NA 403 1_555 D O GLY 48 D GLY 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.167 ? metalc ? metalc20 D O SER 263 D SER 263 1_555 N NA NA . D NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc21 D OG SER 265 D SER 265 1_555 N NA NA . D NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? metalc ? metalc22 D O TYR 301 D TYR 301 1_555 N NA NA . D NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc23 D O GLY 303 D GLY 303 1_555 N NA NA . D NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc24 N NA NA . D NA 402 1_555 R O HOH . D HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? # _chem_comp.formula 'C11 H17 N2 O8 P' _chem_comp.formula_weight 336.235 _chem_comp.id PLS _chem_comp.mon_nstd_flag . _chem_comp.name '[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms PYRIDOXYL-SERINE-5-MONOPHOSPHATE # 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 N CA PLS sing 294 n n N C4A PLS sing 295 n n N HN PLS sing 296 n n CA CB PLS sing 297 n n CA C PLS sing 298 n n CA HA PLS sing 299 n n CB OG PLS sing 300 n n CB HB1 PLS sing 301 n n CB HB2 PLS sing 302 n n OG HOG PLS sing 303 n n C O PLS doub 304 n n C OXT PLS sing 305 n n OXT HXT PLS sing 306 n n N1 C2 PLS doub 307 n y N1 C6 PLS sing 308 n y C2 C2A PLS sing 309 n n C2 C3 PLS sing 310 n y C2A H2A1 PLS sing 311 n n C2A H2A2 PLS sing 312 n n C2A H2A3 PLS sing 313 n n C3 O3 PLS sing 314 n n C3 C4 PLS doub 315 n y O3 HO3 PLS sing 316 n n C4 C4A PLS sing 317 n n C4 C5 PLS sing 318 n y C4A H4A1 PLS sing 319 n n C4A H4A2 PLS sing 320 n n C5 C6 PLS doub 321 n y C5 C5A PLS sing 322 n n C6 H6 PLS sing 323 n n C5A O4P PLS sing 324 n n C5A H5A1 PLS sing 325 n n C5A H5A2 PLS sing 326 n n O4P P PLS sing 327 n n P O1P PLS doub 328 n n P O2P PLS sing 329 n n P O3P PLS sing 330 n n O2P HOP2 PLS sing 331 n n O3P HOP3 PLS sing 332 n n # _atom_sites.entry_id 6AM9 _atom_sites.fract_transf_matrix[1][1] 0.011428 _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] 0.009164 _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] 0.006231 _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 NA A 1 401 2 NA NA . F 2 NA A 1 402 6 NA NA . G 3 PLS A 1 403 1 PLS PLS . H 4 0JO B 1 401 4 0JO 0JO . I 2 NA B 1 402 1 NA NA . J 4 0JO C 1 401 3 0JO 0JO . K 2 NA C 1 402 4 NA NA . L 2 NA C 1 403 7 NA NA . M 4 0JO D 1 401 2 0JO 0JO . N 2 NA D 1 402 3 NA NA . O 5 HOH A 1 501 40 HOH HOH . O 5 HOH A 2 502 37 HOH HOH . O 5 HOH A 3 503 77 HOH HOH . O 5 HOH A 4 504 44 HOH HOH . O 5 HOH A 5 505 46 HOH HOH . O 5 HOH A 6 506 53 HOH HOH . O 5 HOH A 7 507 26 HOH HOH . O 5 HOH A 8 508 95 HOH HOH . O 5 HOH A 9 509 63 HOH HOH . O 5 HOH A 10 510 85 HOH HOH . O 5 HOH A 11 511 100 HOH HOH . O 5 HOH A 12 512 68 HOH HOH . O 5 HOH A 13 513 84 HOH HOH . O 5 HOH A 14 514 117 HOH HOH . O 5 HOH A 15 515 106 HOH HOH . O 5 HOH A 16 516 111 HOH HOH . O 5 HOH A 17 517 75 HOH HOH . O 5 HOH A 18 518 66 HOH HOH . O 5 HOH A 19 519 89 HOH HOH . O 5 HOH A 20 520 59 HOH HOH . P 5 HOH B 1 501 54 HOH HOH . P 5 HOH B 2 502 39 HOH HOH . P 5 HOH B 3 503 48 HOH HOH . P 5 HOH B 4 504 86 HOH HOH . P 5 HOH B 5 505 102 HOH HOH . P 5 HOH B 6 506 99 HOH HOH . P 5 HOH B 7 507 43 HOH HOH . P 5 HOH B 8 508 74 HOH HOH . P 5 HOH B 9 509 56 HOH HOH . P 5 HOH B 10 510 125 HOH HOH . P 5 HOH B 11 511 116 HOH HOH . P 5 HOH B 12 512 61 HOH HOH . P 5 HOH B 13 513 47 HOH HOH . P 5 HOH B 14 514 36 HOH HOH . P 5 HOH B 15 515 120 HOH HOH . P 5 HOH B 16 516 29 HOH HOH . P 5 HOH B 17 517 19 HOH HOH . P 5 HOH B 18 518 64 HOH HOH . P 5 HOH B 19 519 72 HOH HOH . P 5 HOH B 20 520 108 HOH HOH . P 5 HOH B 21 521 82 HOH HOH . P 5 HOH B 22 522 13 HOH HOH . P 5 HOH B 23 523 113 HOH HOH . P 5 HOH B 24 524 12 HOH HOH . Q 5 HOH C 1 501 55 HOH HOH . Q 5 HOH C 2 502 124 HOH HOH . Q 5 HOH C 3 503 51 HOH HOH . Q 5 HOH C 4 504 119 HOH HOH . Q 5 HOH C 5 505 122 HOH HOH . Q 5 HOH C 6 506 107 HOH HOH . Q 5 HOH C 7 507 50 HOH HOH . Q 5 HOH C 8 508 33 HOH HOH . Q 5 HOH C 9 509 25 HOH HOH . Q 5 HOH C 10 510 76 HOH HOH . Q 5 HOH C 11 511 42 HOH HOH . Q 5 HOH C 12 512 109 HOH HOH . Q 5 HOH C 13 513 4 HOH HOH . Q 5 HOH C 14 514 98 HOH HOH . Q 5 HOH C 15 515 57 HOH HOH . Q 5 HOH C 16 516 81 HOH HOH . Q 5 HOH C 17 517 22 HOH HOH . Q 5 HOH C 18 518 112 HOH HOH . Q 5 HOH C 19 519 10 HOH HOH . Q 5 HOH C 20 520 62 HOH HOH . Q 5 HOH C 21 521 18 HOH HOH . Q 5 HOH C 22 522 114 HOH HOH . Q 5 HOH C 23 523 91 HOH HOH . R 5 HOH D 1 501 123 HOH HOH . R 5 HOH D 2 502 60 HOH HOH . R 5 HOH D 3 503 58 HOH HOH . R 5 HOH D 4 504 52 HOH HOH . R 5 HOH D 5 505 78 HOH HOH . R 5 HOH D 6 506 45 HOH HOH . R 5 HOH D 7 507 38 HOH HOH . R 5 HOH D 8 508 41 HOH HOH . R 5 HOH D 9 509 21 HOH HOH . R 5 HOH D 10 510 34 HOH HOH . R 5 HOH D 11 511 70 HOH HOH . R 5 HOH D 12 512 8 HOH HOH . R 5 HOH D 13 513 31 HOH HOH . R 5 HOH D 14 514 97 HOH HOH . R 5 HOH D 15 515 101 HOH HOH . R 5 HOH D 16 516 79 HOH HOH . R 5 HOH D 17 517 121 HOH HOH . R 5 HOH D 18 518 5 HOH HOH . R 5 HOH D 19 519 67 HOH HOH . R 5 HOH D 20 520 3 HOH HOH . R 5 HOH D 21 521 71 HOH HOH . R 5 HOH D 22 522 93 HOH HOH . R 5 HOH D 23 523 73 HOH HOH . R 5 HOH D 24 524 2 HOH HOH . R 5 HOH D 25 525 11 HOH HOH . R 5 HOH D 26 526 110 HOH HOH . R 5 HOH D 27 527 7 HOH HOH . R 5 HOH D 28 528 35 HOH HOH . R 5 HOH D 29 529 94 HOH HOH . R 5 HOH D 30 530 92 HOH HOH . R 5 HOH D 31 531 23 HOH HOH . R 5 HOH D 32 532 96 HOH HOH . R 5 HOH D 33 533 69 HOH HOH . R 5 HOH D 34 534 49 HOH HOH . R 5 HOH D 35 535 104 HOH HOH . R 5 HOH D 36 536 118 HOH HOH . R 5 HOH D 37 537 28 HOH HOH . R 5 HOH D 38 538 24 HOH HOH . R 5 HOH D 39 539 105 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 N PLS . . . G 3 -4.332 -39.287 -14.635 1 47.83 ? N PLS 403 A 1 HETATM 2 C CA PLS . . . G 3 -4.751 -40.363 -13.75 1 49.86 ? CA PLS 403 A 1 HETATM 3 C CB PLS . . . G 3 -5.739 -39.919 -12.659 1 50.23 ? CB PLS 403 A 1 HETATM 4 O OG PLS . . . G 3 -7.009 -39.568 -13.219 1 53.68 ? OG PLS 403 A 1 HETATM 5 C C PLS . . . G 3 -5.329 -41.464 -14.581 1 49.2 ? C PLS 403 A 1 HETATM 6 O O PLS . . . G 3 -5.137 -41.457 -15.818 1 52.1 ? O PLS 403 A 1 HETATM 7 O OXT PLS . . . G 3 -5.978 -42.353 -14.015 1 49.66 ? OXT PLS 403 A 1 HETATM 8 N N1 PLS . . . G 3 -1.697 -35.247 -16.637 1 48.94 ? N1 PLS 403 A 1 HETATM 9 C C2 PLS . . . G 3 -2.387 -36.224 -17.277 1 48.42 ? C2 PLS 403 A 1 HETATM 10 C C2A PLS . . . G 3 -2.364 -36.293 -18.781 1 48.69 ? C2A PLS 403 A 1 HETATM 11 C C3 PLS . . . G 3 -3.162 -37.22 -16.492 1 47.62 ? C3 PLS 403 A 1 HETATM 12 O O3 PLS . . . G 3 -3.862 -38.209 -17.107 1 46.06 ? O3 PLS 403 A 1 HETATM 13 C C4 PLS . . . G 3 -3.135 -37.101 -15.01 1 47.5 ? C4 PLS 403 A 1 HETATM 14 C C4A PLS . . . G 3 -3.891 -38.033 -14.09 1 47.79 ? C4A PLS 403 A 1 HETATM 15 C C5 PLS . . . G 3 -2.342 -35.977 -14.438 1 47.6 ? C5 PLS 403 A 1 HETATM 16 C C6 PLS . . . G 3 -1.659 -35.112 -15.296 1 48.96 ? C6 PLS 403 A 1 HETATM 17 C C5A PLS . . . G 3 -2.264 -35.764 -12.942 1 48.17 ? C5A PLS 403 A 1 HETATM 18 O O4P PLS . . . G 3 -1.582 -36.859 -12.329 1 47.16 ? O4P PLS 403 A 1 HETATM 19 P P PLS . . . G 3 -0.145 -36.682 -11.638 1 45.95 ? P PLS 403 A 1 HETATM 20 O O1P PLS . . . G 3 0.819 -36.311 -12.739 1 48.25 ? O1P PLS 403 A 1 HETATM 21 O O2P PLS . . . G 3 -0.373 -35.554 -10.668 1 47.02 ? O2P PLS 403 A 1 HETATM 22 O O3P PLS . . . G 3 0.127 -38.034 -11.022 1 43.22 ? O3P PLS 403 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 22 #