data_8YIB # _model_server_result.job_id eh3vA8aw2E9MSF8ijzZyDw _model_server_result.datetime_utc '2024-10-11 02:26:39' _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 8yib # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":412}' # _entry.id 8YIB # _exptl.entry_id 8YIB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 12 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 5 _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 8YIB _cell.length_a 132.548 _cell.length_b 132.548 _cell.length_c 249.754 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YIB _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA _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 ? 12 N N N ? 12 O N N ? 12 HA N N ? 12 IA N N ? 12 JA 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 covale ? covale1 A OG SER 130 A SER 116 1_555 G C6 4I1 . A 4I1 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale2 B OG SER 130 B SER 116 1_555 DA C6 4I1 . B 4I1 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? metalc ? metalc1 A OD1 ASP 78 A ASP 64 1_555 K ZN ZN . A ZN 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc2 A OD2 ASP 250 A ASP 236 1_555 K ZN ZN . A ZN 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc3 A O GLY 297 A GLY 283 1_555 L CA CA . A CA 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc4 A OD2 ASP 362 A ASP 348 1_555 L CA CA . A CA 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc5 A OD1 ASP 365 A ASP 351 1_555 L CA CA . A CA 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc6 A OD2 ASP 365 A ASP 351 1_555 L CA CA . A CA 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc7 A OD2 ASP 370 A ASP 356 1_555 L CA CA . A CA 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc8 A OD2 ASP 373 A ASP 359 1_555 L CA CA . A CA 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc9 L CA CA . A CA 410 1_555 RA O HOH . A HOH 547 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc10 M MG MG . A MG 411 1_555 RA O HOH . A HOH 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc11 B OD1 ASP 78 B ASP 64 1_555 FA ZN ZN . B ZN 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc12 B OD2 ASP 78 B ASP 64 1_555 FA ZN ZN . B ZN 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc13 B OD2 ASP 250 B ASP 236 1_555 FA ZN ZN . B ZN 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc14 B O GLY 297 B GLY 283 1_555 GA CA CA . B CA 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc15 B OD2 ASP 362 B ASP 348 1_555 GA CA CA . B CA 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc16 B OD1 ASP 365 B ASP 351 1_555 GA CA CA . B CA 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc17 B OD2 ASP 365 B ASP 351 1_555 GA CA CA . B CA 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc18 B OD2 ASP 370 B ASP 356 1_555 GA CA CA . B CA 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc19 B OD2 ASP 373 B ASP 359 1_555 GA CA CA . B CA 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc20 GA CA CA . B CA 410 1_555 SA O HOH . B HOH 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 O1 GOL sing 249 n n C1 C2 GOL sing 250 n n C1 H11 GOL sing 251 n n C1 H12 GOL sing 252 n n O1 HO1 GOL sing 253 n n C2 O2 GOL sing 254 n n C2 C3 GOL sing 255 n n C2 H2 GOL sing 256 n n O2 HO2 GOL sing 257 n n C3 O3 GOL sing 258 n n C3 H31 GOL sing 259 n n C3 H32 GOL sing 260 n n O3 HO3 GOL sing 261 n n # _atom_sites.entry_id 8YIB _atom_sites.fract_transf_matrix[1][1] 0.007544 _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] 0.007544 _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] 0.004004 _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 FMT A 1 401 404 FMT FMT . D 3 OCA A 1 402 408 OCA OCA . E 4 PPI A 1 403 410 PPI PPI . F 5 ACY A 1 404 411 ACY ACY . G 6 4I1 A 1 405 412 4I1 LIG . H 3 OCA A 1 406 414 OCA OCA . I 7 BUA A 1 407 415 BUA BUA . J 8 DAO A 1 408 416 DAO DAO . K 9 ZN A 1 409 1 ZN ZN . L 10 CA A 1 410 1 CA CA . M 11 MG A 1 411 1 MG MG . N 12 GOL A 1 412 3 GOL GOL . O 12 GOL A 1 413 5 GOL GOL . P 13 6NA A 1 414 504 6NA 6NA . Q 2 FMT A 1 415 601 FMT FMT . R 2 FMT A 1 416 602 FMT FMT . S 2 FMT A 1 417 604 FMT FMT . T 2 FMT A 1 418 605 FMT FMT . U 8 DAO A 1 419 803 DAO DAO . V 14 CL A 1 420 1 CL CL . W 14 CL A 1 421 3 CL CL . X 13 6NA B 1 401 406 6NA 6NA . Y 2 FMT B 1 402 402 FMT FMT . Z 13 6NA B 1 403 405 6NA 6NA . AA 7 BUA B 1 404 406 BUA BUA . BA 3 OCA B 1 405 407 OCA OCA . CA 3 OCA B 1 406 408 OCA OCA . DA 6 4I1 B 1 407 412 4I1 LIG . EA 8 DAO B 1 408 410 DAO DAO . FA 9 ZN B 1 409 2 ZN ZN . GA 10 CA B 1 410 2 CA CA . HA 12 GOL B 1 411 4 GOL GOL . IA 12 GOL B 1 412 6 GOL GOL . JA 12 GOL B 1 413 7 GOL GOL . KA 2 FMT B 1 414 701 FMT FMT . LA 2 FMT B 1 415 702 FMT FMT . MA 2 FMT B 1 416 703 FMT FMT . NA 2 FMT B 1 417 704 FMT FMT . OA 8 DAO B 1 418 802 DAO DAO . PA 14 CL B 1 419 2 CL CL . QA 14 CL B 1 420 4 CL CL . RA 15 HOH A 1 501 79 HOH HOH . RA 15 HOH A 2 502 14 HOH HOH . RA 15 HOH A 3 503 33 HOH HOH . RA 15 HOH A 4 504 57 HOH HOH . RA 15 HOH A 5 505 29 HOH HOH . RA 15 HOH A 6 506 10 HOH HOH . RA 15 HOH A 7 507 88 HOH HOH . RA 15 HOH A 8 508 30 HOH HOH . RA 15 HOH A 9 509 76 HOH HOH . RA 15 HOH A 10 510 95 HOH HOH . RA 15 HOH A 11 511 50 HOH HOH . RA 15 HOH A 12 512 86 HOH HOH . RA 15 HOH A 13 513 44 HOH HOH . RA 15 HOH A 14 514 83 HOH HOH . RA 15 HOH A 15 515 108 HOH HOH . RA 15 HOH A 16 516 7 HOH HOH . RA 15 HOH A 17 517 37 HOH HOH . RA 15 HOH A 18 518 97 HOH HOH . RA 15 HOH A 19 519 92 HOH HOH . RA 15 HOH A 20 520 18 HOH HOH . RA 15 HOH A 21 521 28 HOH HOH . RA 15 HOH A 22 522 25 HOH HOH . RA 15 HOH A 23 523 23 HOH HOH . RA 15 HOH A 24 524 12 HOH HOH . RA 15 HOH A 25 525 78 HOH HOH . RA 15 HOH A 26 526 72 HOH HOH . RA 15 HOH A 27 527 43 HOH HOH . RA 15 HOH A 28 528 70 HOH HOH . RA 15 HOH A 29 529 65 HOH HOH . RA 15 HOH A 30 530 35 HOH HOH . RA 15 HOH A 31 531 82 HOH HOH . RA 15 HOH A 32 532 64 HOH HOH . RA 15 HOH A 33 533 1 HOH HOH . RA 15 HOH A 34 534 73 HOH HOH . RA 15 HOH A 35 535 6 HOH HOH . RA 15 HOH A 36 536 47 HOH HOH . RA 15 HOH A 37 537 61 HOH HOH . RA 15 HOH A 38 538 96 HOH HOH . RA 15 HOH A 39 539 84 HOH HOH . RA 15 HOH A 40 540 59 HOH HOH . RA 15 HOH A 41 541 63 HOH HOH . RA 15 HOH A 42 542 16 HOH HOH . RA 15 HOH A 43 543 56 HOH HOH . RA 15 HOH A 44 544 49 HOH HOH . RA 15 HOH A 45 545 19 HOH HOH . RA 15 HOH A 46 546 26 HOH HOH . RA 15 HOH A 47 547 42 HOH HOH . RA 15 HOH A 48 548 77 HOH HOH . RA 15 HOH A 49 549 51 HOH HOH . RA 15 HOH A 50 550 32 HOH HOH . RA 15 HOH A 51 551 80 HOH HOH . RA 15 HOH A 52 552 98 HOH HOH . RA 15 HOH A 53 553 75 HOH HOH . RA 15 HOH A 54 554 9 HOH HOH . RA 15 HOH A 55 555 55 HOH HOH . RA 15 HOH A 56 556 34 HOH HOH . RA 15 HOH A 57 557 67 HOH HOH . RA 15 HOH A 58 558 114 HOH HOH . RA 15 HOH A 59 559 15 HOH HOH . RA 15 HOH A 60 560 99 HOH HOH . RA 15 HOH A 61 561 3 HOH HOH . RA 15 HOH A 62 562 89 HOH HOH . RA 15 HOH A 63 563 101 HOH HOH . RA 15 HOH A 64 564 17 HOH HOH . RA 15 HOH A 65 565 21 HOH HOH . RA 15 HOH A 66 566 71 HOH HOH . RA 15 HOH A 67 567 69 HOH HOH . RA 15 HOH A 68 568 13 HOH HOH . RA 15 HOH A 69 569 107 HOH HOH . RA 15 HOH A 70 570 115 HOH HOH . RA 15 HOH A 71 571 137 HOH HOH . RA 15 HOH A 72 572 117 HOH HOH . RA 15 HOH A 73 573 113 HOH HOH . RA 15 HOH A 74 574 112 HOH HOH . RA 15 HOH A 75 575 66 HOH HOH . RA 15 HOH A 76 576 100 HOH HOH . RA 15 HOH A 77 577 111 HOH HOH . RA 15 HOH A 78 578 133 HOH HOH . RA 15 HOH A 79 579 109 HOH HOH . RA 15 HOH A 80 580 93 HOH HOH . RA 15 HOH A 81 581 134 HOH HOH . RA 15 HOH A 82 582 118 HOH HOH . RA 15 HOH A 83 583 116 HOH HOH . RA 15 HOH A 84 584 130 HOH HOH . RA 15 HOH A 85 585 58 HOH HOH . RA 15 HOH A 86 586 110 HOH HOH . RA 15 HOH A 87 587 102 HOH HOH . RA 15 HOH A 88 588 104 HOH HOH . RA 15 HOH A 89 589 128 HOH HOH . SA 15 HOH B 1 501 40 HOH HOH . SA 15 HOH B 2 502 31 HOH HOH . SA 15 HOH B 3 503 74 HOH HOH . SA 15 HOH B 4 504 87 HOH HOH . SA 15 HOH B 5 505 60 HOH HOH . SA 15 HOH B 6 506 22 HOH HOH . SA 15 HOH B 7 507 2 HOH HOH . SA 15 HOH B 8 508 27 HOH HOH . SA 15 HOH B 9 509 11 HOH HOH . SA 15 HOH B 10 510 62 HOH HOH . SA 15 HOH B 11 511 20 HOH HOH . SA 15 HOH B 12 512 4 HOH HOH . SA 15 HOH B 13 513 54 HOH HOH . SA 15 HOH B 14 514 90 HOH HOH . SA 15 HOH B 15 515 85 HOH HOH . SA 15 HOH B 16 516 24 HOH HOH . SA 15 HOH B 17 517 68 HOH HOH . SA 15 HOH B 18 518 94 HOH HOH . SA 15 HOH B 19 519 41 HOH HOH . SA 15 HOH B 20 520 46 HOH HOH . SA 15 HOH B 21 521 52 HOH HOH . SA 15 HOH B 22 522 81 HOH HOH . SA 15 HOH B 23 523 39 HOH HOH . SA 15 HOH B 24 524 45 HOH HOH . SA 15 HOH B 25 525 38 HOH HOH . SA 15 HOH B 26 526 129 HOH HOH . SA 15 HOH B 27 527 8 HOH HOH . SA 15 HOH B 28 528 36 HOH HOH . SA 15 HOH B 29 529 124 HOH HOH . SA 15 HOH B 30 530 48 HOH HOH . SA 15 HOH B 31 531 53 HOH HOH . SA 15 HOH B 32 532 125 HOH HOH . SA 15 HOH B 33 533 140 HOH HOH . SA 15 HOH B 34 534 121 HOH HOH . SA 15 HOH B 35 535 122 HOH HOH . SA 15 HOH B 36 536 5 HOH HOH . SA 15 HOH B 37 537 136 HOH HOH . SA 15 HOH B 38 538 119 HOH HOH . SA 15 HOH B 39 539 123 HOH HOH . SA 15 HOH B 40 540 138 HOH HOH . SA 15 HOH B 41 541 139 HOH HOH . SA 15 HOH B 42 542 135 HOH HOH . SA 15 HOH B 43 543 132 HOH HOH . SA 15 HOH B 44 544 127 HOH HOH . SA 15 HOH B 45 545 91 HOH HOH . SA 15 HOH B 46 546 105 HOH HOH . SA 15 HOH B 47 547 120 HOH HOH . SA 15 HOH B 48 548 126 HOH HOH . SA 15 HOH B 49 549 131 HOH HOH . SA 15 HOH B 50 550 103 HOH HOH . SA 15 HOH B 51 551 106 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 C C1 GOL . . . N 12 24.506 51.987 -17.518 1 87.91 ? C1 GOL 412 A 1 HETATM 2 O O1 GOL . . . N 12 25.419 52.365 -16.502 1 69.8 ? O1 GOL 412 A 1 HETATM 3 C C2 GOL . . . N 12 23.367 52.972 -17.667 1 101.63 ? C2 GOL 412 A 1 HETATM 4 O O2 GOL . . . N 12 22.45 52.81 -16.581 1 109.59 ? O2 GOL 412 A 1 HETATM 5 C C3 GOL . . . N 12 22.657 52.795 -18.999 1 102.96 ? C3 GOL 412 A 1 HETATM 6 O O3 GOL . . . N 12 22.064 54.025 -19.461 1 112.71 ? O3 GOL 412 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #