data_1D7V # _model_server_result.job_id V2I1Ai73b3s8ITeaBeU3lQ _model_server_result.datetime_utc '2024-11-14 23:28:44' _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 1d7v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 1D7V # _exptl.entry_id 1D7V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 334.262 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE _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 120 _cell.entry_id 1D7V _cell.length_a 153.2 _cell.length_b 153.2 _cell.length_c 86.9 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D7V _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 76.6 132.675092 0 3 'crystal symmetry operation' 7_555 y,x,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 28.966667 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 76.6 132.675092 28.966667 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 LEU 78 A LEU 78 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc2 A N SER 80 A SER 80 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.708 ? metalc ? metalc3 A OG SER 80 A SER 80 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc4 A O ALA 95 A ALA 95 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? metalc ? metalc5 A O THR 98 A THR 98 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc6 A OG1 THR 98 A THR 98 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.051 ? metalc ? metalc7 A O PRO 99 A PRO 99 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc8 A O LEU 102 A LEU 102 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? metalc ? metalc9 A O THR 303 A THR 303 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? metalc ? metalc10 A O VAL 305 A VAL 305 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc11 A OD1 ASP 307 A ASP 307 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? # _chem_comp.formula 'C12 H19 N2 O7 P' _chem_comp.formula_weight 334.262 _chem_comp.id NMA _chem_comp.mon_nstd_flag . _chem_comp.name N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-PYRIDOXYL-2-METHYLALANINE-5-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 C4 C4A NMA sing 237 n n C4 C5 NMA doub 238 n y C4 C3 NMA sing 239 n y C4A N NMA sing 240 n n C4A H4A1 NMA sing 241 n n C4A H4A2 NMA sing 242 n n P O1P NMA doub 243 n n P O2P NMA sing 244 n n P O3P NMA sing 245 n n P O4P NMA sing 246 n n O2P HOP2 NMA sing 247 n n O3P HOP3 NMA sing 248 n n O4P C5A NMA sing 249 n n C5A C5 NMA sing 250 n n C5A H5A1 NMA sing 251 n n C5A H5A2 NMA sing 252 n n C5 C6 NMA sing 253 n y N1 C6 NMA doub 254 n y N1 C2 NMA sing 255 n y C6 H6 NMA sing 256 n n C2 C2A NMA sing 257 n n C2 C3 NMA doub 258 n y C2A H2A1 NMA sing 259 n n C2A H2A2 NMA sing 260 n n C2A H2A3 NMA sing 261 n n C3 O3 NMA sing 262 n n O3 HO3 NMA sing 263 n n N C8 NMA sing 264 n n N HN NMA sing 265 n n C8 C7 NMA sing 266 n n C8 C9 NMA sing 267 n n C8 C10 NMA sing 268 n n C7 O7 NMA doub 269 n n C7 O8 NMA sing 270 n n O8 HO8 NMA sing 271 n n C9 H91 NMA sing 272 n n C9 H92 NMA sing 273 n n C9 H93 NMA sing 274 n n C10 H101 NMA sing 275 n n C10 H102 NMA sing 276 n n C10 H103 NMA sing 277 n n # _atom_sites.entry_id 1D7V _atom_sites.fract_transf_matrix[1][1] 0.006527 _atom_sites.fract_transf_matrix[1][2] 0.003768 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007537 _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] 0.011507 _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 B 2 NA A 1 435 435 NA NA+ . C 3 K A 1 436 436 K K+ . D 4 NMA A 1 500 500 NMA PMA . E 5 HOH A 1 501 501 HOH WAT . E 5 HOH A 2 502 502 HOH WAT . E 5 HOH A 3 503 503 HOH WAT . E 5 HOH A 4 505 505 HOH WAT . E 5 HOH A 5 507 507 HOH WAT . E 5 HOH A 6 508 508 HOH WAT . E 5 HOH A 7 509 509 HOH WAT . E 5 HOH A 8 512 512 HOH WAT . E 5 HOH A 9 514 514 HOH WAT . E 5 HOH A 10 517 517 HOH WAT . E 5 HOH A 11 518 518 HOH WAT . E 5 HOH A 12 519 519 HOH WAT . E 5 HOH A 13 520 520 HOH WAT . E 5 HOH A 14 521 521 HOH WAT . E 5 HOH A 15 524 524 HOH WAT . E 5 HOH A 16 528 528 HOH WAT . E 5 HOH A 17 531 531 HOH WAT . E 5 HOH A 18 533 533 HOH WAT . E 5 HOH A 19 535 535 HOH WAT . E 5 HOH A 20 536 536 HOH WAT . E 5 HOH A 21 539 539 HOH WAT . E 5 HOH A 22 540 540 HOH WAT . E 5 HOH A 23 544 544 HOH WAT . E 5 HOH A 24 545 545 HOH WAT . E 5 HOH A 25 546 546 HOH WAT . E 5 HOH A 26 548 548 HOH WAT . E 5 HOH A 27 552 552 HOH WAT . E 5 HOH A 28 553 553 HOH WAT . E 5 HOH A 29 560 560 HOH WAT . E 5 HOH A 30 561 561 HOH WAT . E 5 HOH A 31 563 563 HOH WAT . E 5 HOH A 32 564 564 HOH WAT . E 5 HOH A 33 565 565 HOH WAT . E 5 HOH A 34 566 566 HOH WAT . E 5 HOH A 35 567 567 HOH WAT . E 5 HOH A 36 568 500 HOH PMA . # 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 C C4 NMA . . . D 4 17.156 52.452 16.613 1 14.86 ? C4 NMA 500 A 1 HETATM 2 C C4A NMA . . . D 4 17.133 52.016 17.981 1 43.25 ? C4A NMA 500 A 1 HETATM 3 P P NMA . . . D 4 20.402 48.794 16.681 1 30.96 ? P NMA 500 A 1 HETATM 4 O O1P NMA . . . D 4 21.852 48.854 16.273 1 100 ? O1P NMA 500 A 1 HETATM 5 O O2P NMA . . . D 4 20.295 49.415 18.121 1 63.31 ? O2P NMA 500 A 1 HETATM 6 O O3P NMA . . . D 4 19.702 47.493 16.575 1 56.5 ? O3P NMA 500 A 1 HETATM 7 O O4P NMA . . . D 4 19.564 49.832 15.815 1 83.3 ? O4P NMA 500 A 1 HETATM 8 C C5A NMA . . . D 4 19.29 51.076 16.462 1 40.24 ? C5A NMA 500 A 1 HETATM 9 C C5 NMA . . . D 4 18.253 52.009 15.802 1 47.7 ? C5 NMA 500 A 1 HETATM 10 N N1 NMA . . . D 4 17.579 53.342 14.048 1 33.74 ? N1 NMA 500 A 1 HETATM 11 C C6 NMA . . . D 4 18.467 52.473 14.545 1 43.37 ? C6 NMA 500 A 1 HETATM 12 C C2 NMA . . . D 4 16.486 53.809 14.728 1 11.54 ? C2 NMA 500 A 1 HETATM 13 C C2A NMA . . . D 4 15.587 54.792 14.022 1 54.28 ? C2A NMA 500 A 1 HETATM 14 C C3 NMA . . . D 4 16.285 53.398 16.07 1 37.24 ? C3 NMA 500 A 1 HETATM 15 O O3 NMA . . . D 4 15.222 53.965 16.721 1 41.44 ? O3 NMA 500 A 1 HETATM 16 N N NMA . . . D 4 16.095 51.621 18.609 1 42.19 ? N NMA 500 A 1 HETATM 17 C C8 NMA . . . D 4 16.05 51.775 20.086 1 58.12 ? C8 NMA 500 A 1 HETATM 18 C C7 NMA . . . D 4 14.749 52.396 20.443 1 34.61 ? C7 NMA 500 A 1 HETATM 19 O O7 NMA . . . D 4 13.622 51.736 20.267 1 97 ? O7 NMA 500 A 1 HETATM 20 O O8 NMA . . . D 4 14.751 53.553 20.83 1 100 ? O8 NMA 500 A 1 HETATM 21 C C9 NMA . . . D 4 16.251 50.523 20.949 1 43.53 ? C9 NMA 500 A 1 HETATM 22 C C10 NMA . . . D 4 17.107 52.827 20.481 1 52.9 ? C10 NMA 500 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 400 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #