data_3PBF # _model_server_result.job_id ez0Lel6vVVRPBerbww7byA _model_server_result.datetime_utc '2024-11-24 19:57:38' _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 3pbf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":412}' # _entry.id 3PBF # _exptl.entry_id 3PBF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 3 _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 3PBF _cell.length_a 97.376 _cell.length_b 97.376 _cell.length_c 44.905 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PBF _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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 97.376 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 48.688 84.33009 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E 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 disulf ? disulf1 A SG CYS 55 A CYS 135 1_555 A SG CYS 146 A CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 124 A CYS 204 1_555 A SG CYS 138 A CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 A OE1 GLU 115 A GLU 195 1_555 B CA CA . A CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc2 A OE1 GLU 122 A GLU 202 1_555 B CA CA . A CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? metalc ? metalc3 A OD1 ASN 134 A ASN 214 1_555 B CA CA . A CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? metalc ? metalc4 A OD1 ASP 135 A ASP 215 1_555 B CA CA . A CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc5 A O ASP 135 A ASP 215 1_555 B CA CA . A CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc6 B CA CA . A CA 300 1_555 E O2 GOL . A GOL 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? metalc ? metalc7 B CA CA . A CA 300 1_555 E O1 GOL . A GOL 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? metalc ? metalc8 B CA CA . A CA 300 1_555 F O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? # _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 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 3PBF _atom_sites.fract_transf_matrix[1][1] 0.010269 _atom_sites.fract_transf_matrix[1][2] 0.005929 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011858 _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] 0.022269 _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 CA A 1 300 300 CA CA . C 3 GOL A 1 410 410 GOL GOL . D 3 GOL A 1 411 411 GOL GOL . E 3 GOL A 1 412 412 GOL GOL . F 4 HOH A 1 413 413 HOH HOH . F 4 HOH A 2 414 414 HOH HOH . F 4 HOH A 3 415 415 HOH HOH . F 4 HOH A 4 416 416 HOH HOH . F 4 HOH A 5 417 417 HOH HOH . F 4 HOH A 6 418 418 HOH HOH . F 4 HOH A 7 419 419 HOH HOH . F 4 HOH A 8 420 420 HOH HOH . F 4 HOH A 9 421 421 HOH HOH . F 4 HOH A 10 422 422 HOH HOH . F 4 HOH A 11 423 423 HOH HOH . F 4 HOH A 12 424 424 HOH HOH . F 4 HOH A 13 425 425 HOH HOH . F 4 HOH A 14 426 426 HOH HOH . F 4 HOH A 15 427 427 HOH HOH . F 4 HOH A 16 428 428 HOH HOH . F 4 HOH A 17 429 429 HOH HOH . F 4 HOH A 18 430 430 HOH HOH . F 4 HOH A 19 431 431 HOH HOH . F 4 HOH A 20 432 432 HOH HOH . F 4 HOH A 21 433 433 HOH HOH . F 4 HOH A 22 434 434 HOH HOH . F 4 HOH A 23 435 435 HOH HOH . F 4 HOH A 24 436 436 HOH HOH . F 4 HOH A 25 437 437 HOH HOH . F 4 HOH A 26 438 438 HOH HOH . F 4 HOH A 27 439 439 HOH HOH . F 4 HOH A 28 440 440 HOH HOH . F 4 HOH A 29 441 441 HOH HOH . F 4 HOH A 30 442 442 HOH HOH . F 4 HOH A 31 443 443 HOH HOH . F 4 HOH A 32 444 444 HOH HOH . F 4 HOH A 33 445 445 HOH HOH . F 4 HOH A 34 446 446 HOH HOH . F 4 HOH A 35 447 447 HOH HOH . F 4 HOH A 36 448 448 HOH HOH . F 4 HOH A 37 449 449 HOH HOH . F 4 HOH A 38 450 450 HOH HOH . F 4 HOH A 39 451 451 HOH HOH . F 4 HOH A 40 452 452 HOH HOH . F 4 HOH A 41 453 453 HOH HOH . F 4 HOH A 42 454 454 HOH HOH . F 4 HOH A 43 455 455 HOH HOH . F 4 HOH A 44 456 456 HOH HOH . F 4 HOH A 45 457 457 HOH HOH . F 4 HOH A 46 458 458 HOH HOH . F 4 HOH A 47 459 459 HOH HOH . F 4 HOH A 48 460 460 HOH HOH . F 4 HOH A 49 461 461 HOH HOH . F 4 HOH A 50 462 462 HOH HOH . F 4 HOH A 51 463 463 HOH HOH . F 4 HOH A 52 464 464 HOH HOH . F 4 HOH A 53 465 465 HOH HOH . F 4 HOH A 54 466 466 HOH HOH . F 4 HOH A 55 467 467 HOH HOH . F 4 HOH A 56 468 468 HOH HOH . F 4 HOH A 57 469 469 HOH HOH . F 4 HOH A 58 470 470 HOH HOH . F 4 HOH A 59 471 471 HOH HOH . F 4 HOH A 60 472 472 HOH HOH . F 4 HOH A 61 473 473 HOH HOH . F 4 HOH A 62 474 474 HOH HOH . F 4 HOH A 63 475 475 HOH HOH . F 4 HOH A 64 476 476 HOH HOH . F 4 HOH A 65 477 477 HOH HOH . F 4 HOH A 66 478 478 HOH HOH . F 4 HOH A 67 479 479 HOH HOH . F 4 HOH A 68 480 480 HOH HOH . F 4 HOH A 69 481 481 HOH HOH . F 4 HOH A 70 482 482 HOH HOH . F 4 HOH A 71 483 483 HOH HOH . F 4 HOH A 72 484 484 HOH HOH . F 4 HOH A 73 485 485 HOH HOH . F 4 HOH A 74 486 486 HOH HOH . F 4 HOH A 75 487 487 HOH HOH . F 4 HOH A 76 488 488 HOH HOH . F 4 HOH A 77 489 489 HOH HOH . F 4 HOH A 78 490 490 HOH HOH . F 4 HOH A 79 491 491 HOH HOH . F 4 HOH A 80 492 492 HOH HOH . F 4 HOH A 81 493 493 HOH HOH . F 4 HOH A 82 494 494 HOH HOH . F 4 HOH A 83 495 495 HOH HOH . F 4 HOH A 84 496 496 HOH HOH . F 4 HOH A 85 497 497 HOH HOH . F 4 HOH A 86 498 498 HOH HOH . F 4 HOH A 87 499 499 HOH HOH . F 4 HOH A 88 500 500 HOH HOH . F 4 HOH A 89 501 501 HOH HOH . F 4 HOH A 90 502 502 HOH HOH . F 4 HOH A 91 503 503 HOH HOH . F 4 HOH A 92 504 504 HOH HOH . F 4 HOH A 93 505 505 HOH HOH . F 4 HOH A 94 506 506 HOH HOH . F 4 HOH A 95 507 507 HOH HOH . F 4 HOH A 96 508 508 HOH HOH . F 4 HOH A 97 509 509 HOH HOH . F 4 HOH A 98 510 510 HOH HOH . F 4 HOH A 99 511 511 HOH HOH . F 4 HOH A 100 512 512 HOH HOH . F 4 HOH A 101 513 513 HOH HOH . F 4 HOH A 102 514 514 HOH HOH . F 4 HOH A 103 515 515 HOH HOH . F 4 HOH A 104 516 516 HOH HOH . F 4 HOH A 105 517 517 HOH HOH . F 4 HOH A 106 518 518 HOH HOH . F 4 HOH A 107 519 519 HOH HOH . F 4 HOH A 108 520 520 HOH HOH . F 4 HOH A 109 521 521 HOH HOH . F 4 HOH A 110 522 522 HOH HOH . F 4 HOH A 111 523 523 HOH HOH . F 4 HOH A 112 524 524 HOH HOH . F 4 HOH A 113 525 525 HOH HOH . F 4 HOH A 114 526 526 HOH HOH . F 4 HOH A 115 527 527 HOH HOH . F 4 HOH A 116 528 528 HOH HOH . F 4 HOH A 117 529 529 HOH HOH . F 4 HOH A 118 530 530 HOH HOH . F 4 HOH A 119 531 531 HOH HOH . F 4 HOH A 120 532 532 HOH HOH . F 4 HOH A 121 533 533 HOH HOH . F 4 HOH A 122 534 534 HOH HOH . F 4 HOH A 123 535 535 HOH HOH . F 4 HOH A 124 536 536 HOH HOH . F 4 HOH A 125 537 537 HOH HOH . F 4 HOH A 126 538 538 HOH HOH . F 4 HOH A 127 539 539 HOH HOH . F 4 HOH A 128 540 540 HOH HOH . F 4 HOH A 129 541 541 HOH HOH . F 4 HOH A 130 542 542 HOH HOH . F 4 HOH A 131 543 543 HOH HOH . F 4 HOH A 132 544 544 HOH HOH . F 4 HOH A 133 545 545 HOH HOH . F 4 HOH A 134 546 546 HOH HOH . F 4 HOH A 135 547 547 HOH HOH . F 4 HOH A 136 548 548 HOH HOH . F 4 HOH A 137 549 549 HOH HOH . F 4 HOH A 138 550 550 HOH HOH . F 4 HOH A 139 551 551 HOH HOH . F 4 HOH A 140 552 552 HOH HOH . F 4 HOH A 141 553 553 HOH HOH . F 4 HOH A 142 554 554 HOH HOH . F 4 HOH A 143 555 555 HOH HOH . F 4 HOH A 144 556 556 HOH HOH . F 4 HOH A 145 557 557 HOH HOH . F 4 HOH A 146 558 558 HOH HOH . F 4 HOH A 147 559 559 HOH HOH . F 4 HOH A 148 560 560 HOH HOH . F 4 HOH A 149 561 561 HOH HOH . F 4 HOH A 150 562 562 HOH HOH . F 4 HOH A 151 563 563 HOH HOH . F 4 HOH A 152 564 564 HOH HOH . F 4 HOH A 153 565 565 HOH HOH . F 4 HOH A 154 566 566 HOH HOH . F 4 HOH A 155 567 567 HOH HOH . F 4 HOH A 156 568 568 HOH HOH . F 4 HOH A 157 569 569 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 . . . E 3 82.121 37.187 50.117 1 29.63 ? C1 GOL 412 A 1 HETATM 2 O O1 GOL . . . E 3 83.097 37.602 49.171 1 25.53 ? O1 GOL 412 A 1 HETATM 3 C C2 GOL . . . E 3 82.216 35.686 50.403 1 31.08 ? C2 GOL 412 A 1 HETATM 4 O O2 GOL . . . E 3 82.026 34.916 49.207 1 30.66 ? O2 GOL 412 A 1 HETATM 5 C C3 GOL . . . E 3 81.159 35.312 51.44 1 32.84 ? C3 GOL 412 A 1 HETATM 6 O O3 GOL . . . E 3 81.215 33.927 51.731 1 35.95 ? O3 GOL 412 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #