data_1YTE # _model_server_result.job_id zofw3DTceoNfAb0aNV_lKg _model_server_result.datetime_utc '2024-11-14 23:52:16' _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 1yte # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 1YTE # _exptl.entry_id 1YTE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 388.097 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE _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 1YTE _cell.length_a 136.061 _cell.length_b 136.061 _cell.length_c 120.166 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YTE _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 _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 1 136.061 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 68.0305 117.832282 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 68.0305 117.832282 60.083 5 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 136.061 0 60.083 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 60.083 # _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 # 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 39 A CYS 33 1_555 A SG CYS 106 A CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 336 A CYS 330 1_555 A SG CYS 354 A CYS 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? # _chem_comp.formula 'C6 H15 O13 P3' _chem_comp.formula_weight 388.097 _chem_comp.id PCP _chem_comp.mon_nstd_flag . _chem_comp.name 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'CARBOXYLIC PRPP;CPRPP' # 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 C1 C2 PCP sing 237 n n C1 C5 PCP sing 238 n n C1 O1 PCP sing 239 n n C1 H1 PCP sing 240 n n C2 C3 PCP sing 241 n n C2 O2 PCP sing 242 n n C2 H2 PCP sing 243 n n C3 C4 PCP sing 244 n n C3 O3 PCP sing 245 n n C3 H3 PCP sing 246 n n C4 C5 PCP sing 247 n n C4 CP PCP sing 248 n n C4 H4 PCP sing 249 n n C5 H51 PCP sing 250 n n C5 H52 PCP sing 251 n n CP OP PCP sing 252 n n CP HP1 PCP sing 253 n n CP HP2 PCP sing 254 n n O1 PA PCP sing 255 n n O2 HO2 PCP sing 256 n n O3 HO3 PCP sing 257 n n OP P PCP sing 258 n n P O1P PCP doub 259 n n P O2P PCP sing 260 n n P O3P PCP sing 261 n n O2P HOP2 PCP sing 262 n n O3P HOP3 PCP sing 263 n n PA O1A PCP doub 264 n n PA O2A PCP sing 265 n n PA O3A PCP sing 266 n n O2A HOA2 PCP sing 267 n n O3A PB PCP sing 268 n n PB O1B PCP doub 269 n n PB O2B PCP sing 270 n n PB O3B PCP sing 271 n n O2B HOB2 PCP sing 272 n n O3B HOB3 PCP sing 273 n n # _atom_sites.entry_id 1YTE _atom_sites.fract_transf_matrix[1][1] 0.00735 _atom_sites.fract_transf_matrix[1][2] 0.004243 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008487 _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] 0.008322 _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 PCP A 1 401 401 PCP PCP . C 3 HOH A 1 501 501 HOH TIP . C 3 HOH A 2 502 502 HOH TIP . C 3 HOH A 3 503 503 HOH TIP . C 3 HOH A 4 504 504 HOH TIP . C 3 HOH A 5 505 505 HOH TIP . C 3 HOH A 6 506 506 HOH TIP . C 3 HOH A 7 507 507 HOH TIP . C 3 HOH A 8 508 508 HOH TIP . C 3 HOH A 9 509 509 HOH TIP . C 3 HOH A 10 510 510 HOH TIP . C 3 HOH A 11 511 511 HOH TIP . C 3 HOH A 12 512 512 HOH TIP . C 3 HOH A 13 513 513 HOH TIP . C 3 HOH A 14 514 514 HOH TIP . C 3 HOH A 15 515 515 HOH TIP . C 3 HOH A 16 516 516 HOH TIP . C 3 HOH A 17 517 517 HOH TIP . C 3 HOH A 18 518 518 HOH TIP . C 3 HOH A 19 519 519 HOH TIP . C 3 HOH A 20 520 520 HOH TIP . C 3 HOH A 21 521 521 HOH TIP . C 3 HOH A 22 522 522 HOH TIP . C 3 HOH A 23 523 523 HOH TIP . C 3 HOH A 24 524 524 HOH TIP . C 3 HOH A 25 525 525 HOH TIP . C 3 HOH A 26 526 526 HOH TIP . C 3 HOH A 27 527 527 HOH TIP . C 3 HOH A 28 528 528 HOH TIP . C 3 HOH A 29 529 529 HOH TIP . C 3 HOH A 30 530 530 HOH TIP . C 3 HOH A 31 531 531 HOH TIP . C 3 HOH A 32 532 532 HOH TIP . C 3 HOH A 33 533 533 HOH TIP . C 3 HOH A 34 534 534 HOH TIP . C 3 HOH A 35 535 535 HOH TIP . C 3 HOH A 36 536 536 HOH TIP . C 3 HOH A 37 537 537 HOH TIP . C 3 HOH A 38 538 538 HOH TIP . C 3 HOH A 39 539 539 HOH TIP . C 3 HOH A 40 540 540 HOH TIP . C 3 HOH A 41 541 541 HOH TIP . C 3 HOH A 42 542 542 HOH TIP . C 3 HOH A 43 543 543 HOH TIP . C 3 HOH A 44 544 544 HOH TIP . C 3 HOH A 45 545 545 HOH TIP . C 3 HOH A 46 546 546 HOH TIP . C 3 HOH A 47 547 547 HOH TIP . C 3 HOH A 48 548 548 HOH TIP . C 3 HOH A 49 549 549 HOH TIP . C 3 HOH A 50 550 550 HOH TIP . C 3 HOH A 51 551 551 HOH TIP . C 3 HOH A 52 552 552 HOH TIP . C 3 HOH A 53 553 553 HOH TIP . C 3 HOH A 54 554 554 HOH TIP . C 3 HOH A 55 555 555 HOH TIP . C 3 HOH A 56 556 556 HOH TIP . C 3 HOH A 57 557 557 HOH TIP . C 3 HOH A 58 558 558 HOH TIP . C 3 HOH A 59 559 559 HOH TIP . C 3 HOH A 60 560 560 HOH TIP . C 3 HOH A 61 561 561 HOH TIP . C 3 HOH A 62 562 562 HOH TIP . C 3 HOH A 63 563 563 HOH TIP . C 3 HOH A 64 564 564 HOH TIP . C 3 HOH A 65 565 565 HOH TIP . C 3 HOH A 66 566 566 HOH TIP . C 3 HOH A 67 567 567 HOH TIP . C 3 HOH A 68 568 568 HOH TIP . C 3 HOH A 69 569 569 HOH TIP . C 3 HOH A 70 570 570 HOH TIP . C 3 HOH A 71 571 571 HOH TIP . C 3 HOH A 72 572 572 HOH TIP . C 3 HOH A 73 573 573 HOH TIP . C 3 HOH A 74 574 574 HOH TIP . C 3 HOH A 75 575 575 HOH TIP . C 3 HOH A 76 576 576 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 C C1 PCP . . . B 2 81.394 65.658 30.088 1 97.75 ? C1 PCP 401 A 1 HETATM 2 C C2 PCP . . . B 2 81.071 64.218 29.643 1 97.06 ? C2 PCP 401 A 1 HETATM 3 C C3 PCP . . . B 2 82.201 63.327 30.226 1 94.38 ? C3 PCP 401 A 1 HETATM 4 C C4 PCP . . . B 2 83.414 64.249 30.461 1 91.76 ? C4 PCP 401 A 1 HETATM 5 C C5 PCP . . . B 2 82.796 65.603 30.554 1 94.89 ? C5 PCP 401 A 1 HETATM 6 C CP PCP . . . B 2 84.484 64.18 29.357 1 85.69 ? CP PCP 401 A 1 HETATM 7 O O1 PCP . . . B 2 80.618 66.031 31.327 1 102.12 ? O1 PCP 401 A 1 HETATM 8 O O2 PCP . . . B 2 79.774 63.82 30.123 1 98.41 ? O2 PCP 401 A 1 HETATM 9 O O3 PCP . . . B 2 81.88 62.705 31.474 1 95.46 ? O3 PCP 401 A 1 HETATM 10 O OP PCP . . . B 2 83.936 64.531 28.067 1 76.39 ? OP PCP 401 A 1 HETATM 11 P P PCP . . . B 2 84.806 64.653 26.744 1 70.68 ? P PCP 401 A 1 HETATM 12 O O1P PCP . . . B 2 84.086 63.918 25.696 1 71.83 ? O1P PCP 401 A 1 HETATM 13 O O2P PCP . . . B 2 86.112 64.051 27.046 1 70.93 ? O2P PCP 401 A 1 HETATM 14 O O3P PCP . . . B 2 84.897 66.105 26.47 1 71.81 ? O3P PCP 401 A 1 HETATM 15 P PA PCP . . . B 2 80.65 67.418 32.086 1 106.11 ? PA PCP 401 A 1 HETATM 16 O O1A PCP . . . B 2 80.454 68.492 31.044 1 106.66 ? O1A PCP 401 A 1 HETATM 17 O O2A PCP . . . B 2 81.993 67.534 32.755 1 105.21 ? O2A PCP 401 A 1 HETATM 18 O O3A PCP . . . B 2 79.475 67.237 33.028 1 105.34 ? O3A PCP 401 A 1 HETATM 19 P PB PCP . . . B 2 78.291 66.282 33.052 1 105.43 ? PB PCP 401 A 1 HETATM 20 O O1B PCP . . . B 2 77.319 66.643 34.119 1 107.13 ? O1B PCP 401 A 1 HETATM 21 O O2B PCP . . . B 2 78.711 64.92 33.306 1 103.69 ? O2B PCP 401 A 1 HETATM 22 O O3B PCP . . . B 2 77.584 66.265 31.734 1 105.47 ? O3B PCP 401 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 399 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 22 #