data_5VNS # _model_server_result.job_id fkj18Tv3EE2Kpk3n3aDfXQ _model_server_result.datetime_utc '2025-01-26 00:23:29' _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 5vns # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 5VNS # _exptl.entry_id 5VNS _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 2 _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 5VNS _cell.length_a 68.379 _cell.length_b 122.784 _cell.length_c 40.256 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VNS _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 ? 3 C N N ? 3 D N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id OG _struct_conn.ptnr1_label_comp_id SER _struct_conn.ptnr1_label_seq_id 125 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id SER _struct_conn.ptnr1_auth_seq_id 124 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C1' _struct_conn.ptnr2_label_comp_id DH9 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id DH9 _struct_conn.ptnr2_auth_seq_id 401 _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 1.4 _struct_conn.pdbx_value_order ? # _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 340 n n C1 H11 MPD sing 341 n n C1 H12 MPD sing 342 n n C1 H13 MPD sing 343 n n C2 O2 MPD sing 344 n n C2 CM MPD sing 345 n n C2 C3 MPD sing 346 n n O2 HO2 MPD sing 347 n n CM HM1 MPD sing 348 n n CM HM2 MPD sing 349 n n CM HM3 MPD sing 350 n n C3 C4 MPD sing 351 n n C3 H31 MPD sing 352 n n C3 H32 MPD sing 353 n n C4 O4 MPD sing 354 n n C4 C5 MPD sing 355 n n C4 H4 MPD sing 356 n n O4 HO4 MPD sing 357 n n C5 H51 MPD sing 358 n n C5 H52 MPD sing 359 n n C5 H53 MPD sing 360 n n # _atom_sites.entry_id 5VNS _atom_sites.fract_transf_matrix[1][1] 0.014624 _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] 0.008144 _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] 0.024841 _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 DH9 A 1 401 124 DH9 DH9 . C 3 MPD A 1 402 1 MPD MPD . D 3 MPD A 1 403 2 MPD MPD . E 4 GOL A 1 404 3 GOL GOL . F 4 GOL A 1 405 4 GOL GOL . G 5 HOH A 1 501 213 HOH HOH . G 5 HOH A 2 502 237 HOH HOH . G 5 HOH A 3 503 129 HOH HOH . G 5 HOH A 4 504 179 HOH HOH . G 5 HOH A 5 505 144 HOH HOH . G 5 HOH A 6 506 115 HOH HOH . G 5 HOH A 7 507 235 HOH HOH . G 5 HOH A 8 508 98 HOH HOH . G 5 HOH A 9 509 52 HOH HOH . G 5 HOH A 10 510 12 HOH HOH . G 5 HOH A 11 511 118 HOH HOH . G 5 HOH A 12 512 91 HOH HOH . G 5 HOH A 13 513 14 HOH HOH . G 5 HOH A 14 514 136 HOH HOH . G 5 HOH A 15 515 210 HOH HOH . G 5 HOH A 16 516 177 HOH HOH . G 5 HOH A 17 517 9 HOH HOH . G 5 HOH A 18 518 67 HOH HOH . G 5 HOH A 19 519 205 HOH HOH . G 5 HOH A 20 520 244 HOH HOH . G 5 HOH A 21 521 142 HOH HOH . G 5 HOH A 22 522 163 HOH HOH . G 5 HOH A 23 523 28 HOH HOH . G 5 HOH A 24 524 30 HOH HOH . G 5 HOH A 25 525 120 HOH HOH . G 5 HOH A 26 526 85 HOH HOH . G 5 HOH A 27 527 1 HOH HOH . G 5 HOH A 28 528 20 HOH HOH . G 5 HOH A 29 529 206 HOH HOH . G 5 HOH A 30 530 194 HOH HOH . G 5 HOH A 31 531 113 HOH HOH . G 5 HOH A 32 532 226 HOH HOH . G 5 HOH A 33 533 51 HOH HOH . G 5 HOH A 34 534 150 HOH HOH . G 5 HOH A 35 535 233 HOH HOH . G 5 HOH A 36 536 11 HOH HOH . G 5 HOH A 37 537 289 HOH HOH . G 5 HOH A 38 538 79 HOH HOH . G 5 HOH A 39 539 38 HOH HOH . G 5 HOH A 40 540 24 HOH HOH . G 5 HOH A 41 541 21 HOH HOH . G 5 HOH A 42 542 148 HOH HOH . G 5 HOH A 43 543 108 HOH HOH . G 5 HOH A 44 544 43 HOH HOH . G 5 HOH A 45 545 50 HOH HOH . G 5 HOH A 46 546 88 HOH HOH . G 5 HOH A 47 547 215 HOH HOH . G 5 HOH A 48 548 169 HOH HOH . G 5 HOH A 49 549 18 HOH HOH . G 5 HOH A 50 550 60 HOH HOH . G 5 HOH A 51 551 8 HOH HOH . G 5 HOH A 52 552 101 HOH HOH . G 5 HOH A 53 553 106 HOH HOH . G 5 HOH A 54 554 109 HOH HOH . G 5 HOH A 55 555 36 HOH HOH . G 5 HOH A 56 556 119 HOH HOH . G 5 HOH A 57 557 121 HOH HOH . G 5 HOH A 58 558 48 HOH HOH . G 5 HOH A 59 559 73 HOH HOH . G 5 HOH A 60 560 165 HOH HOH . G 5 HOH A 61 561 45 HOH HOH . G 5 HOH A 62 562 87 HOH HOH . G 5 HOH A 63 563 158 HOH HOH . G 5 HOH A 64 564 100 HOH HOH . G 5 HOH A 65 565 239 HOH HOH . G 5 HOH A 66 566 83 HOH HOH . G 5 HOH A 67 567 4 HOH HOH . G 5 HOH A 68 568 133 HOH HOH . G 5 HOH A 69 569 286 HOH HOH . G 5 HOH A 70 570 72 HOH HOH . G 5 HOH A 71 571 2 HOH HOH . G 5 HOH A 72 572 13 HOH HOH . G 5 HOH A 73 573 32 HOH HOH . G 5 HOH A 74 574 94 HOH HOH . G 5 HOH A 75 575 29 HOH HOH . G 5 HOH A 76 576 187 HOH HOH . G 5 HOH A 77 577 92 HOH HOH . G 5 HOH A 78 578 107 HOH HOH . G 5 HOH A 79 579 46 HOH HOH . G 5 HOH A 80 580 182 HOH HOH . G 5 HOH A 81 581 10 HOH HOH . G 5 HOH A 82 582 5 HOH HOH . G 5 HOH A 83 583 37 HOH HOH . G 5 HOH A 84 584 69 HOH HOH . G 5 HOH A 85 585 138 HOH HOH . G 5 HOH A 86 586 58 HOH HOH . G 5 HOH A 87 587 15 HOH HOH . G 5 HOH A 88 588 130 HOH HOH . G 5 HOH A 89 589 26 HOH HOH . G 5 HOH A 90 590 253 HOH HOH . G 5 HOH A 91 591 39 HOH HOH . G 5 HOH A 92 592 7 HOH HOH . G 5 HOH A 93 593 146 HOH HOH . G 5 HOH A 94 594 124 HOH HOH . G 5 HOH A 95 595 77 HOH HOH . G 5 HOH A 96 596 17 HOH HOH . G 5 HOH A 97 597 66 HOH HOH . G 5 HOH A 98 598 281 HOH HOH . G 5 HOH A 99 599 267 HOH HOH . G 5 HOH A 100 600 68 HOH HOH . G 5 HOH A 101 601 41 HOH HOH . G 5 HOH A 102 602 155 HOH HOH . G 5 HOH A 103 603 280 HOH HOH . G 5 HOH A 104 604 6 HOH HOH . G 5 HOH A 105 605 126 HOH HOH . G 5 HOH A 106 606 104 HOH HOH . G 5 HOH A 107 607 241 HOH HOH . G 5 HOH A 108 608 81 HOH HOH . G 5 HOH A 109 609 116 HOH HOH . G 5 HOH A 110 610 218 HOH HOH . G 5 HOH A 111 611 135 HOH HOH . G 5 HOH A 112 612 191 HOH HOH . G 5 HOH A 113 613 63 HOH HOH . G 5 HOH A 114 614 47 HOH HOH . G 5 HOH A 115 615 137 HOH HOH . G 5 HOH A 116 616 40 HOH HOH . G 5 HOH A 117 617 3 HOH HOH . G 5 HOH A 118 618 62 HOH HOH . G 5 HOH A 119 619 95 HOH HOH . G 5 HOH A 120 620 49 HOH HOH . G 5 HOH A 121 621 70 HOH HOH . G 5 HOH A 122 622 123 HOH HOH . G 5 HOH A 123 623 196 HOH HOH . G 5 HOH A 124 624 99 HOH HOH . G 5 HOH A 125 625 42 HOH HOH . G 5 HOH A 126 626 84 HOH HOH . G 5 HOH A 127 627 114 HOH HOH . G 5 HOH A 128 628 23 HOH HOH . G 5 HOH A 129 629 245 HOH HOH . G 5 HOH A 130 630 64 HOH HOH . G 5 HOH A 131 631 97 HOH HOH . G 5 HOH A 132 632 22 HOH HOH . G 5 HOH A 133 633 229 HOH HOH . G 5 HOH A 134 634 35 HOH HOH . G 5 HOH A 135 635 242 HOH HOH . G 5 HOH A 136 636 86 HOH HOH . G 5 HOH A 137 637 16 HOH HOH . G 5 HOH A 138 638 82 HOH HOH . G 5 HOH A 139 639 199 HOH HOH . G 5 HOH A 140 640 112 HOH HOH . G 5 HOH A 141 641 55 HOH HOH . G 5 HOH A 142 642 65 HOH HOH . G 5 HOH A 143 643 160 HOH HOH . G 5 HOH A 144 644 61 HOH HOH . G 5 HOH A 145 645 287 HOH HOH . G 5 HOH A 146 646 143 HOH HOH . G 5 HOH A 147 647 54 HOH HOH . G 5 HOH A 148 648 154 HOH HOH . G 5 HOH A 149 649 93 HOH HOH . G 5 HOH A 150 650 200 HOH HOH . G 5 HOH A 151 651 174 HOH HOH . G 5 HOH A 152 652 59 HOH HOH . G 5 HOH A 153 653 71 HOH HOH . G 5 HOH A 154 654 252 HOH HOH . G 5 HOH A 155 655 263 HOH HOH . G 5 HOH A 156 656 76 HOH HOH . G 5 HOH A 157 657 157 HOH HOH . G 5 HOH A 158 658 152 HOH HOH . G 5 HOH A 159 659 259 HOH HOH . G 5 HOH A 160 660 149 HOH HOH . G 5 HOH A 161 661 25 HOH HOH . G 5 HOH A 162 662 173 HOH HOH . G 5 HOH A 163 663 141 HOH HOH . G 5 HOH A 164 664 105 HOH HOH . G 5 HOH A 165 665 27 HOH HOH . G 5 HOH A 166 666 57 HOH HOH . G 5 HOH A 167 667 178 HOH HOH . G 5 HOH A 168 668 175 HOH HOH . G 5 HOH A 169 669 151 HOH HOH . G 5 HOH A 170 670 80 HOH HOH . G 5 HOH A 171 671 222 HOH HOH . G 5 HOH A 172 672 19 HOH HOH . G 5 HOH A 173 673 90 HOH HOH . G 5 HOH A 174 674 127 HOH HOH . G 5 HOH A 175 675 273 HOH HOH . G 5 HOH A 176 676 161 HOH HOH . G 5 HOH A 177 677 170 HOH HOH . G 5 HOH A 178 678 134 HOH HOH . G 5 HOH A 179 679 266 HOH HOH . G 5 HOH A 180 680 211 HOH HOH . G 5 HOH A 181 681 227 HOH HOH . G 5 HOH A 182 682 209 HOH HOH . G 5 HOH A 183 683 128 HOH HOH . G 5 HOH A 184 684 172 HOH HOH . G 5 HOH A 185 685 181 HOH HOH . G 5 HOH A 186 686 232 HOH HOH . G 5 HOH A 187 687 132 HOH HOH . G 5 HOH A 188 688 284 HOH HOH . G 5 HOH A 189 689 180 HOH HOH . G 5 HOH A 190 690 89 HOH HOH . G 5 HOH A 191 691 111 HOH HOH . G 5 HOH A 192 692 74 HOH HOH . G 5 HOH A 193 693 278 HOH HOH . G 5 HOH A 194 694 162 HOH HOH . G 5 HOH A 195 695 153 HOH HOH . G 5 HOH A 196 696 220 HOH HOH . G 5 HOH A 197 697 167 HOH HOH . G 5 HOH A 198 698 110 HOH HOH . G 5 HOH A 199 699 44 HOH HOH . G 5 HOH A 200 700 139 HOH HOH . G 5 HOH A 201 701 131 HOH HOH . G 5 HOH A 202 702 53 HOH HOH . G 5 HOH A 203 703 204 HOH HOH . G 5 HOH A 204 704 260 HOH HOH . G 5 HOH A 205 705 247 HOH HOH . G 5 HOH A 206 706 225 HOH HOH . G 5 HOH A 207 707 140 HOH HOH . G 5 HOH A 208 708 56 HOH HOH . G 5 HOH A 209 709 198 HOH HOH . G 5 HOH A 210 710 221 HOH HOH . G 5 HOH A 211 711 193 HOH HOH . G 5 HOH A 212 712 256 HOH HOH . G 5 HOH A 213 713 96 HOH HOH . G 5 HOH A 214 714 283 HOH HOH . G 5 HOH A 215 715 186 HOH HOH . G 5 HOH A 216 716 240 HOH HOH . G 5 HOH A 217 717 243 HOH HOH . G 5 HOH A 218 718 166 HOH HOH . G 5 HOH A 219 719 33 HOH HOH . G 5 HOH A 220 720 183 HOH HOH . G 5 HOH A 221 721 216 HOH HOH . G 5 HOH A 222 722 262 HOH HOH . G 5 HOH A 223 723 34 HOH HOH . G 5 HOH A 224 724 275 HOH HOH . G 5 HOH A 225 725 272 HOH HOH . G 5 HOH A 226 726 254 HOH HOH . G 5 HOH A 227 727 156 HOH HOH . G 5 HOH A 228 728 288 HOH HOH . G 5 HOH A 229 729 197 HOH HOH . G 5 HOH A 230 730 248 HOH HOH . G 5 HOH A 231 731 255 HOH HOH . G 5 HOH A 232 732 230 HOH HOH . G 5 HOH A 233 733 276 HOH HOH . G 5 HOH A 234 734 234 HOH HOH . G 5 HOH A 235 735 171 HOH HOH . G 5 HOH A 236 736 279 HOH HOH . G 5 HOH A 237 737 285 HOH HOH . G 5 HOH A 238 738 214 HOH HOH . G 5 HOH A 239 739 274 HOH HOH . G 5 HOH A 240 740 147 HOH HOH . G 5 HOH A 241 741 122 HOH HOH . G 5 HOH A 242 742 201 HOH HOH . G 5 HOH A 243 743 250 HOH HOH . G 5 HOH A 244 744 290 HOH HOH . G 5 HOH A 245 745 168 HOH HOH . G 5 HOH A 246 746 190 HOH HOH . G 5 HOH A 247 747 176 HOH HOH . G 5 HOH A 248 748 117 HOH HOH . G 5 HOH A 249 749 145 HOH HOH . G 5 HOH A 250 750 270 HOH HOH . G 5 HOH A 251 751 264 HOH HOH . G 5 HOH A 252 752 223 HOH HOH . G 5 HOH A 253 753 265 HOH HOH . G 5 HOH A 254 754 258 HOH HOH . G 5 HOH A 255 755 203 HOH HOH . G 5 HOH A 256 756 75 HOH HOH . G 5 HOH A 257 757 268 HOH HOH . G 5 HOH A 258 758 291 HOH HOH . G 5 HOH A 259 759 207 HOH HOH . G 5 HOH A 260 760 246 HOH HOH . G 5 HOH A 261 761 188 HOH HOH . G 5 HOH A 262 762 261 HOH HOH . G 5 HOH A 263 763 238 HOH HOH . G 5 HOH A 264 764 164 HOH HOH . G 5 HOH A 265 765 189 HOH HOH . G 5 HOH A 266 766 125 HOH HOH . G 5 HOH A 267 767 282 HOH HOH . G 5 HOH A 268 768 78 HOH HOH . G 5 HOH A 269 769 103 HOH HOH . G 5 HOH A 270 770 271 HOH HOH . G 5 HOH A 271 771 219 HOH HOH . G 5 HOH A 272 772 236 HOH HOH . G 5 HOH A 273 773 269 HOH HOH . G 5 HOH A 274 774 257 HOH HOH . G 5 HOH A 275 775 249 HOH HOH . G 5 HOH A 276 776 277 HOH HOH . G 5 HOH A 277 777 251 HOH HOH . G 5 HOH A 278 778 217 HOH HOH . G 5 HOH A 279 779 202 HOH HOH . G 5 HOH A 280 780 228 HOH HOH . G 5 HOH A 281 781 208 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 . . . D 3 38.536 126.076 -36.771 1 37.74 ? C1 MPD 403 A 1 HETATM 2 C C2 MPD . . . D 3 39.023 126.585 -35.436 1 39.88 ? C2 MPD 403 A 1 HETATM 3 O O2 MPD . . . D 3 38.851 125.575 -34.489 1 41.93 ? O2 MPD 403 A 1 HETATM 4 C CM MPD . . . D 3 40.491 126.845 -35.423 1 39.59 ? CM MPD 403 A 1 HETATM 5 C C3 MPD . . . D 3 38.289 127.773 -34.864 1 39.85 ? C3 MPD 403 A 1 HETATM 6 C C4 MPD . . . D 3 37.214 128.557 -35.596 1 32.85 ? C4 MPD 403 A 1 HETATM 7 O O4 MPD . . . D 3 36.571 127.918 -36.667 1 34.3 ? O4 MPD 403 A 1 HETATM 8 C C5 MPD . . . D 3 36.164 128.902 -34.559 1 30.29 ? C5 MPD 403 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 356 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 8 #