data_1YTK # _model_server_result.job_id RJb-5E_Q3_0uwEINYV8ZZg _model_server_result.datetime_utc '2024-11-30 05:27:07' _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 1ytk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 1YTK # _exptl.entry_id 1YTK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 335.204 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICOTINATE MONONUCLEOTIDE' _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 1YTK _cell.length_a 135.191 _cell.length_b 135.191 _cell.length_c 119.66 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YTK _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 135.191 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 67.5955 117.07884 0 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 67.5955 117.07884 59.83 5 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 135.191 0 59.83 6 'crystal symmetry operation' 12_555 x,x-y,-z+1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 59.83 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 39 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 33 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 106 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 100 _struct_conn.ptnr2_symmetry 1_555 _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 2.035 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C11 H14 N O9 P' _chem_comp.formula_weight 335.204 _chem_comp.id NCN _chem_comp.mon_nstd_flag . _chem_comp.name 'NICOTINATE MONONUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms NAMN # 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 P O1P NCN sing 237 n n P O2P NCN doub 238 n n P O3P NCN sing 239 n n P O5' NCN sing 240 n n O1P HOP1 NCN sing 241 n n O5' C5' NCN sing 242 n n C5' C4' NCN sing 243 n n C5' "H5'1" NCN sing 244 n n C5' "H5'2" NCN sing 245 n n C4' O4' NCN sing 246 n n C4' C3' NCN sing 247 n n C4' H4' NCN sing 248 n n O4' C1' NCN sing 249 n n C3' O3' NCN sing 250 n n C3' C2' NCN sing 251 n n C3' H3' NCN sing 252 n n O3' "HO'3" NCN sing 253 n n C2' O2' NCN sing 254 n n C2' C1' NCN sing 255 n n C2' H2' NCN sing 256 n n O2' "HO'2" NCN sing 257 n n C1' N1 NCN sing 258 n n C1' H1' NCN sing 259 n n N1 C6 NCN sing 260 n y N1 C2 NCN doub 261 n y C6 C5 NCN doub 262 n y C6 H6 NCN sing 263 n n C5 C4 NCN sing 264 n y C5 H5 NCN sing 265 n n C4 C3 NCN doub 266 n y C4 H4 NCN sing 267 n n C3 C2 NCN sing 268 n y C3 C7 NCN sing 269 n n C2 H2 NCN sing 270 n n C7 O7 NCN sing 271 n n C7 O8 NCN doub 272 n n O7 HO7 NCN sing 273 n n # _atom_sites.entry_id 1YTK _atom_sites.fract_transf_matrix[1][1] 0.007397 _atom_sites.fract_transf_matrix[1][2] 0.004271 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008541 _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] 0.008357 _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 NCN A 1 401 401 NCN NCN . C 3 TRS A 1 402 402 TRS TRS . D 4 HOH A 1 501 501 HOH TIP . D 4 HOH A 2 502 502 HOH TIP . D 4 HOH A 3 503 503 HOH TIP . D 4 HOH A 4 504 504 HOH TIP . D 4 HOH A 5 505 505 HOH TIP . D 4 HOH A 6 506 506 HOH TIP . D 4 HOH A 7 507 507 HOH TIP . D 4 HOH A 8 508 508 HOH TIP . D 4 HOH A 9 509 509 HOH TIP . D 4 HOH A 10 510 510 HOH TIP . D 4 HOH A 11 511 511 HOH TIP . D 4 HOH A 12 512 512 HOH TIP . D 4 HOH A 13 513 513 HOH TIP . D 4 HOH A 14 514 514 HOH TIP . D 4 HOH A 15 515 515 HOH TIP . D 4 HOH A 16 516 516 HOH TIP . D 4 HOH A 17 517 517 HOH TIP . D 4 HOH A 18 518 518 HOH TIP . D 4 HOH A 19 519 519 HOH TIP . D 4 HOH A 20 520 520 HOH TIP . D 4 HOH A 21 521 521 HOH TIP . D 4 HOH A 22 522 522 HOH TIP . D 4 HOH A 23 523 523 HOH TIP . D 4 HOH A 24 524 524 HOH TIP . D 4 HOH A 25 525 525 HOH TIP . D 4 HOH A 26 526 526 HOH TIP . D 4 HOH A 27 527 527 HOH TIP . D 4 HOH A 28 528 528 HOH TIP . D 4 HOH A 29 529 529 HOH TIP . D 4 HOH A 30 530 530 HOH TIP . D 4 HOH A 31 531 531 HOH TIP . D 4 HOH A 32 532 532 HOH TIP . D 4 HOH A 33 533 533 HOH TIP . D 4 HOH A 34 534 534 HOH TIP . D 4 HOH A 35 535 535 HOH TIP . D 4 HOH A 36 536 536 HOH TIP . D 4 HOH A 37 537 537 HOH TIP . D 4 HOH A 38 538 538 HOH TIP . D 4 HOH A 39 539 539 HOH TIP . D 4 HOH A 40 540 540 HOH TIP . D 4 HOH A 41 541 541 HOH TIP . D 4 HOH A 42 542 542 HOH TIP . D 4 HOH A 43 543 543 HOH TIP . D 4 HOH A 44 544 544 HOH TIP . D 4 HOH A 45 545 545 HOH TIP . D 4 HOH A 46 546 546 HOH TIP . D 4 HOH A 47 547 547 HOH TIP . D 4 HOH A 48 548 548 HOH TIP . D 4 HOH A 49 549 549 HOH TIP . D 4 HOH A 50 550 550 HOH TIP . D 4 HOH A 51 551 551 HOH TIP . D 4 HOH A 52 552 552 HOH TIP . D 4 HOH A 53 553 553 HOH TIP . D 4 HOH A 54 554 554 HOH TIP . D 4 HOH A 55 555 555 HOH TIP . D 4 HOH A 56 556 556 HOH TIP . D 4 HOH A 57 557 557 HOH TIP . D 4 HOH A 58 558 558 HOH TIP . D 4 HOH A 59 559 559 HOH TIP . D 4 HOH A 60 560 560 HOH TIP . D 4 HOH A 61 561 561 HOH TIP . D 4 HOH A 62 562 562 HOH TIP . D 4 HOH A 63 563 563 HOH TIP . D 4 HOH A 64 564 564 HOH TIP . # 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 P P NCN . . . B 2 84.576 64.62 26.859 1 51.13 ? P NCN 401 A 1 HETATM 2 O O1P NCN . . . B 2 84.164 64.052 25.533 1 50.08 ? O1P NCN 401 A 1 HETATM 3 O O2P NCN . . . B 2 85.538 63.692 27.519 1 51.92 ? O2P NCN 401 A 1 HETATM 4 O O3P NCN . . . B 2 83.277 64.859 27.805 1 50.66 ? O3P NCN 401 A 1 HETATM 5 O O5' NCN . . . B 2 85.345 66.006 26.618 1 55.21 ? O5' NCN 401 A 1 HETATM 6 C C5' NCN . . . B 2 84.542 67.011 26.022 1 56.95 ? C5' NCN 401 A 1 HETATM 7 C C4' NCN . . . B 2 84.464 68.182 26.87 1 56.87 ? C4' NCN 401 A 1 HETATM 8 O O4' NCN . . . B 2 85.808 68.918 27.04 1 55.42 ? O4' NCN 401 A 1 HETATM 9 C C3' NCN . . . B 2 83.48 69.154 26.265 1 56.52 ? C3' NCN 401 A 1 HETATM 10 O O3' NCN . . . B 2 82.515 69.595 27.247 1 55.8 ? O3' NCN 401 A 1 HETATM 11 C C2' NCN . . . B 2 84.309 70.309 25.694 1 56.4 ? C2' NCN 401 A 1 HETATM 12 O O2' NCN . . . B 2 83.689 71.574 26.013 1 59.98 ? O2' NCN 401 A 1 HETATM 13 C C1' NCN . . . B 2 85.722 70.111 26.28 1 54.23 ? C1' NCN 401 A 1 HETATM 14 N N1 NCN . . . B 2 86.911 70.369 25.331 1 49.75 ? N1 NCN 401 A 1 HETATM 15 C C6 NCN . . . B 2 88.096 69.524 25.238 1 48.87 ? C6 NCN 401 A 1 HETATM 16 C C5 NCN . . . B 2 89.063 69.982 24.284 1 45.73 ? C5 NCN 401 A 1 HETATM 17 C C4 NCN . . . B 2 88.946 71.152 23.44 1 43.92 ? C4 NCN 401 A 1 HETATM 18 C C3 NCN . . . B 2 87.674 71.907 23.639 1 45.26 ? C3 NCN 401 A 1 HETATM 19 C C2 NCN . . . B 2 86.705 71.523 24.562 1 47.07 ? C2 NCN 401 A 1 HETATM 20 C C7 NCN . . . B 2 87.645 73.121 22.664 1 45.16 ? C7 NCN 401 A 1 HETATM 21 O O7 NCN . . . B 2 88.477 73.459 21.864 1 46.51 ? O7 NCN 401 A 1 HETATM 22 O O8 NCN . . . B 2 86.492 73.781 22.834 1 41.38 ? O8 NCN 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #