data_3DM9 # _model_server_result.job_id wbbiKH1m9lGf8FA1CraVIQ _model_server_result.datetime_utc '2024-11-26 01:39:08' _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 3dm9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 3DM9 # _exptl.entry_id 3DM9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _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 3DM9 _cell.length_a 144.6 _cell.length_b 144.6 _cell.length_c 70.413 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DM9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 177 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 6 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA hexameric 6 software_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1,2,3,4,5,6 A,B,C,D,E,F,G 2 1 # 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 1 144.6 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 72.3 125.227273 0 4 'crystal symmetry operation' 10_666 -y+1,-x+1,-z+1 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 72.3 125.227273 70.413 5 'crystal symmetry operation' 11_656 -x+y+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 144.6 0 70.413 6 'crystal symmetry operation' 12_556 x,x-y,-z+1 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 70.413 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id F _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 covale ? covale1 A C SER 6 B SER 0 1_555 A N MSE 7 B MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale2 A C MSE 7 B MSE 1 1_555 A N PHE 8 B PHE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 A C ILE 132 B ILE 126 1_555 A N MSE 133 B MSE 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C MSE 133 B MSE 127 1_555 A N PHE 134 B PHE 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C LEU 229 B LEU 223 1_555 A N MSE 230 B MSE 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale6 A C MSE 230 B MSE 224 1_555 A N ASP 231 B ASP 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 A C GLU 232 B GLU 226 1_555 A N MSE 233 B MSE 227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale8 A C MSE 233 B MSE 227 1_555 A N LYS 234 B LYS 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 MPD sing 205 n n C1 H11 MPD sing 206 n n C1 H12 MPD sing 207 n n C1 H13 MPD sing 208 n n C2 O2 MPD sing 209 n n C2 CM MPD sing 210 n n C2 C3 MPD sing 211 n n O2 HO2 MPD sing 212 n n CM HM1 MPD sing 213 n n CM HM2 MPD sing 214 n n CM HM3 MPD sing 215 n n C3 C4 MPD sing 216 n n C3 H31 MPD sing 217 n n C3 H32 MPD sing 218 n n C4 O4 MPD sing 219 n n C4 C5 MPD sing 220 n n C4 H4 MPD sing 221 n n O4 HO4 MPD sing 222 n n C5 H51 MPD sing 223 n n C5 H52 MPD sing 224 n n C5 H53 MPD sing 225 n n # _atom_sites.entry_id 3DM9 _atom_sites.fract_transf_matrix[1][1] 0.006916 _atom_sites.fract_transf_matrix[1][2] 0.003993 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007985 _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] 0.014202 _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 PO4 B 1 323 1 PO4 PO4 . C 2 PO4 B 1 324 2 PO4 PO4 . D 2 PO4 B 1 325 3 PO4 PO4 . E 2 PO4 B 1 326 4 PO4 PO4 . F 3 MPD B 1 501 501 MPD MPD . G 4 HOH B 1 502 1 HOH HOH . G 4 HOH B 2 503 2 HOH HOH . G 4 HOH B 3 504 3 HOH HOH . G 4 HOH B 4 505 4 HOH HOH . G 4 HOH B 5 506 5 HOH HOH . G 4 HOH B 6 507 6 HOH HOH . G 4 HOH B 7 508 7 HOH HOH . G 4 HOH B 8 509 8 HOH HOH . G 4 HOH B 9 510 9 HOH HOH . G 4 HOH B 10 511 10 HOH HOH . G 4 HOH B 11 512 11 HOH HOH . G 4 HOH B 12 513 12 HOH HOH . G 4 HOH B 13 514 13 HOH HOH . G 4 HOH B 14 515 14 HOH HOH . G 4 HOH B 15 516 15 HOH HOH . G 4 HOH B 16 517 16 HOH HOH . G 4 HOH B 17 518 17 HOH HOH . G 4 HOH B 18 519 18 HOH HOH . G 4 HOH B 19 520 19 HOH HOH . G 4 HOH B 20 521 20 HOH HOH . G 4 HOH B 21 522 21 HOH HOH . G 4 HOH B 22 523 22 HOH HOH . G 4 HOH B 23 524 23 HOH HOH . G 4 HOH B 24 525 24 HOH HOH . G 4 HOH B 25 526 25 HOH HOH . G 4 HOH B 26 527 26 HOH HOH . G 4 HOH B 27 528 27 HOH HOH . G 4 HOH B 28 529 28 HOH HOH . G 4 HOH B 29 530 29 HOH HOH . G 4 HOH B 30 531 30 HOH HOH . G 4 HOH B 31 532 31 HOH HOH . G 4 HOH B 32 533 32 HOH HOH . G 4 HOH B 33 534 33 HOH HOH . G 4 HOH B 34 535 34 HOH HOH . G 4 HOH B 35 536 35 HOH HOH . G 4 HOH B 36 537 36 HOH HOH . G 4 HOH B 37 538 37 HOH HOH . G 4 HOH B 38 539 38 HOH HOH . G 4 HOH B 39 540 39 HOH HOH . G 4 HOH B 40 541 40 HOH HOH . G 4 HOH B 41 542 41 HOH HOH . G 4 HOH B 42 543 42 HOH HOH . G 4 HOH B 43 544 43 HOH HOH . G 4 HOH B 44 545 44 HOH HOH . G 4 HOH B 45 546 45 HOH HOH . G 4 HOH B 46 547 46 HOH HOH . G 4 HOH B 47 548 47 HOH HOH . G 4 HOH B 48 549 48 HOH HOH . G 4 HOH B 49 550 49 HOH HOH . G 4 HOH B 50 551 50 HOH HOH . G 4 HOH B 51 552 51 HOH HOH . G 4 HOH B 52 553 52 HOH HOH . G 4 HOH B 53 554 53 HOH HOH . G 4 HOH B 54 555 54 HOH HOH . G 4 HOH B 55 556 55 HOH HOH . G 4 HOH B 56 557 56 HOH HOH . G 4 HOH B 57 558 57 HOH HOH . G 4 HOH B 58 559 58 HOH HOH . G 4 HOH B 59 560 59 HOH HOH . G 4 HOH B 60 561 60 HOH HOH . G 4 HOH B 61 562 61 HOH HOH . G 4 HOH B 62 563 62 HOH HOH . G 4 HOH B 63 564 63 HOH HOH . G 4 HOH B 64 565 64 HOH HOH . G 4 HOH B 65 566 65 HOH HOH . G 4 HOH B 66 567 66 HOH HOH . G 4 HOH B 67 568 67 HOH HOH . G 4 HOH B 68 569 68 HOH HOH . G 4 HOH B 69 570 69 HOH HOH . G 4 HOH B 70 571 70 HOH HOH . G 4 HOH B 71 572 71 HOH HOH . G 4 HOH B 72 573 72 HOH HOH . G 4 HOH B 73 574 73 HOH HOH . G 4 HOH B 74 575 74 HOH HOH . G 4 HOH B 75 576 75 HOH HOH . G 4 HOH B 76 577 76 HOH HOH . G 4 HOH B 77 578 77 HOH HOH . G 4 HOH B 78 579 78 HOH HOH . G 4 HOH B 79 580 79 HOH HOH . G 4 HOH B 80 581 80 HOH HOH . G 4 HOH B 81 582 81 HOH HOH . G 4 HOH B 82 583 82 HOH HOH . G 4 HOH B 83 584 83 HOH HOH . G 4 HOH B 84 585 84 HOH HOH . G 4 HOH B 85 586 85 HOH HOH . G 4 HOH B 86 587 86 HOH HOH . G 4 HOH B 87 588 87 HOH HOH . G 4 HOH B 88 589 88 HOH HOH . G 4 HOH B 89 590 89 HOH HOH . G 4 HOH B 90 591 90 HOH HOH . G 4 HOH B 91 592 91 HOH HOH . G 4 HOH B 92 593 92 HOH HOH . G 4 HOH B 93 594 93 HOH HOH . G 4 HOH B 94 595 94 HOH HOH . G 4 HOH B 95 596 95 HOH HOH . G 4 HOH B 96 597 96 HOH HOH . G 4 HOH B 97 598 97 HOH HOH . G 4 HOH B 98 599 98 HOH HOH . G 4 HOH B 99 600 99 HOH HOH . G 4 HOH B 100 601 100 HOH HOH . G 4 HOH B 101 602 101 HOH HOH . G 4 HOH B 102 603 102 HOH HOH . G 4 HOH B 103 604 103 HOH HOH . G 4 HOH B 104 605 104 HOH HOH . G 4 HOH B 105 606 105 HOH HOH . G 4 HOH B 106 607 106 HOH HOH . G 4 HOH B 107 608 107 HOH HOH . G 4 HOH B 108 609 108 HOH HOH . G 4 HOH B 109 610 109 HOH HOH . G 4 HOH B 110 611 110 HOH HOH . G 4 HOH B 111 612 111 HOH HOH . G 4 HOH B 112 613 112 HOH HOH . G 4 HOH B 113 614 113 HOH HOH . G 4 HOH B 114 615 114 HOH HOH . G 4 HOH B 115 616 115 HOH HOH . G 4 HOH B 116 617 116 HOH HOH . G 4 HOH B 117 618 117 HOH HOH . G 4 HOH B 118 619 118 HOH HOH . G 4 HOH B 119 620 119 HOH HOH . G 4 HOH B 120 621 120 HOH HOH . G 4 HOH B 121 622 121 HOH HOH . G 4 HOH B 122 623 122 HOH HOH . G 4 HOH B 123 624 123 HOH HOH . G 4 HOH B 124 625 124 HOH HOH . G 4 HOH B 125 626 125 HOH HOH . G 4 HOH B 126 627 126 HOH HOH . G 4 HOH B 127 628 127 HOH HOH . G 4 HOH B 128 629 128 HOH HOH . G 4 HOH B 129 630 129 HOH HOH . G 4 HOH B 130 631 130 HOH HOH . G 4 HOH B 131 632 131 HOH HOH . G 4 HOH B 132 633 132 HOH HOH . G 4 HOH B 133 634 133 HOH HOH . G 4 HOH B 134 635 134 HOH HOH . G 4 HOH B 135 636 135 HOH HOH . G 4 HOH B 136 637 136 HOH HOH . G 4 HOH B 137 638 137 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 MPD . . . F 3 68.096 59.975 19.548 1 66.67 ? C1 MPD 501 B 1 HETATM 2 C C2 MPD . . . F 3 67.705 59.888 18.084 1 23.17 ? C2 MPD 501 B 1 HETATM 3 O O2 MPD . . . F 3 67.354 58.515 17.82 1 46.9 ? O2 MPD 501 B 1 HETATM 4 C CM MPD . . . F 3 66.492 60.723 17.777 1 35.24 ? CM MPD 501 B 1 HETATM 5 C C3 MPD . . . F 3 68.908 60.334 17.297 1 55.4 ? C3 MPD 501 B 1 HETATM 6 C C4 MPD . . . F 3 68.88 59.972 15.83 1 70.67 ? C4 MPD 501 B 1 HETATM 7 O O4 MPD . . . F 3 67.548 59.706 15.449 1 55.64 ? O4 MPD 501 B 1 HETATM 8 C C5 MPD . . . F 3 69.491 61.139 15.059 1 25.01 ? C5 MPD 501 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 8 #