data_5N3D # _model_server_result.job_id tQQlyoulVbBVbDikmfh_Dg _model_server_result.datetime_utc '2024-11-28 12:21:55' _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 5n3d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 5N3D # _exptl.entry_id 5N3D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 4 _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 90 _cell.entry_id 5N3D _cell.length_a 58.419 _cell.length_b 72.389 _cell.length_c 108.383 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5N3D _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 GLY 12 A GLY 9 1_555 A N SEP 13 A SEP 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C SEP 13 A SEP 10 1_555 A N GLU 14 A GLU 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C PHE 141 A PHE 138 1_555 A N SEP 142 A SEP 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C SEP 142 A SEP 139 1_555 A N GLU 143 A GLU 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale5 A C TRP 199 A TRP 196 1_555 A N TPO 200 A TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale6 A C TPO 200 A TPO 197 1_555 A N LEU 201 A LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 A C VAL 340 A VAL 337 1_555 A N SEP 341 A SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C SEP 341 A SEP 338 1_555 A N ILE 342 A ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _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 258 n n C1 H11 MPD sing 259 n n C1 H12 MPD sing 260 n n C1 H13 MPD sing 261 n n C2 O2 MPD sing 262 n n C2 CM MPD sing 263 n n C2 C3 MPD sing 264 n n O2 HO2 MPD sing 265 n n CM HM1 MPD sing 266 n n CM HM2 MPD sing 267 n n CM HM3 MPD sing 268 n n C3 C4 MPD sing 269 n n C3 H31 MPD sing 270 n n C3 H32 MPD sing 271 n n C4 O4 MPD sing 272 n n C4 C5 MPD sing 273 n n C4 H4 MPD sing 274 n n O4 HO4 MPD sing 275 n n C5 H51 MPD sing 276 n n C5 H52 MPD sing 277 n n C5 H53 MPD sing 278 n n # _atom_sites.entry_id 5N3D _atom_sites.fract_transf_matrix[1][1] 0.017118 _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] 0.013814 _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] 0.009227 _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 3 8NE A 1 401 1 8NE XXX . D 4 MPD A 1 402 1 MPD MPD . E 5 HOH A 1 501 193 HOH HOH . E 5 HOH A 2 502 92 HOH HOH . E 5 HOH A 3 503 188 HOH HOH . E 5 HOH A 4 504 175 HOH HOH . E 5 HOH A 5 505 176 HOH HOH . E 5 HOH A 6 506 190 HOH HOH . E 5 HOH A 7 507 170 HOH HOH . E 5 HOH A 8 508 180 HOH HOH . E 5 HOH A 9 509 195 HOH HOH . E 5 HOH A 10 510 120 HOH HOH . E 5 HOH A 11 511 103 HOH HOH . E 5 HOH A 12 512 212 HOH HOH . E 5 HOH A 13 513 42 HOH HOH . E 5 HOH A 14 514 90 HOH HOH . E 5 HOH A 15 515 210 HOH HOH . E 5 HOH A 16 516 108 HOH HOH . E 5 HOH A 17 517 200 HOH HOH . E 5 HOH A 18 518 153 HOH HOH . E 5 HOH A 19 519 182 HOH HOH . E 5 HOH A 20 520 67 HOH HOH . E 5 HOH A 21 521 95 HOH HOH . E 5 HOH A 22 522 82 HOH HOH . E 5 HOH A 23 523 96 HOH HOH . E 5 HOH A 24 524 222 HOH HOH . E 5 HOH A 25 525 85 HOH HOH . E 5 HOH A 26 526 118 HOH HOH . E 5 HOH A 27 527 146 HOH HOH . E 5 HOH A 28 528 134 HOH HOH . E 5 HOH A 29 529 9 HOH HOH . E 5 HOH A 30 530 48 HOH HOH . E 5 HOH A 31 531 219 HOH HOH . E 5 HOH A 32 532 10 HOH HOH . E 5 HOH A 33 533 121 HOH HOH . E 5 HOH A 34 534 54 HOH HOH . E 5 HOH A 35 535 228 HOH HOH . E 5 HOH A 36 536 34 HOH HOH . E 5 HOH A 37 537 35 HOH HOH . E 5 HOH A 38 538 115 HOH HOH . E 5 HOH A 39 539 61 HOH HOH . E 5 HOH A 40 540 159 HOH HOH . E 5 HOH A 41 541 147 HOH HOH . E 5 HOH A 42 542 109 HOH HOH . E 5 HOH A 43 543 47 HOH HOH . E 5 HOH A 44 544 41 HOH HOH . E 5 HOH A 45 545 99 HOH HOH . E 5 HOH A 46 546 75 HOH HOH . E 5 HOH A 47 547 71 HOH HOH . E 5 HOH A 48 548 4 HOH HOH . E 5 HOH A 49 549 80 HOH HOH . E 5 HOH A 50 550 30 HOH HOH . E 5 HOH A 51 551 68 HOH HOH . E 5 HOH A 52 552 84 HOH HOH . E 5 HOH A 53 553 132 HOH HOH . E 5 HOH A 54 554 49 HOH HOH . E 5 HOH A 55 555 86 HOH HOH . E 5 HOH A 56 556 198 HOH HOH . E 5 HOH A 57 557 32 HOH HOH . E 5 HOH A 58 558 51 HOH HOH . E 5 HOH A 59 559 59 HOH HOH . E 5 HOH A 60 560 43 HOH HOH . E 5 HOH A 61 561 36 HOH HOH . E 5 HOH A 62 562 44 HOH HOH . E 5 HOH A 63 563 52 HOH HOH . E 5 HOH A 64 564 28 HOH HOH . E 5 HOH A 65 565 139 HOH HOH . E 5 HOH A 66 566 169 HOH HOH . E 5 HOH A 67 567 136 HOH HOH . E 5 HOH A 68 568 27 HOH HOH . E 5 HOH A 69 569 24 HOH HOH . E 5 HOH A 70 570 70 HOH HOH . E 5 HOH A 71 571 15 HOH HOH . E 5 HOH A 72 572 23 HOH HOH . E 5 HOH A 73 573 186 HOH HOH . E 5 HOH A 74 574 12 HOH HOH . E 5 HOH A 75 575 13 HOH HOH . E 5 HOH A 76 576 143 HOH HOH . E 5 HOH A 77 577 31 HOH HOH . E 5 HOH A 78 578 140 HOH HOH . E 5 HOH A 79 579 25 HOH HOH . E 5 HOH A 80 580 160 HOH HOH . E 5 HOH A 81 581 40 HOH HOH . E 5 HOH A 82 582 214 HOH HOH . E 5 HOH A 83 583 151 HOH HOH . E 5 HOH A 84 584 204 HOH HOH . E 5 HOH A 85 585 141 HOH HOH . E 5 HOH A 86 586 224 HOH HOH . E 5 HOH A 87 587 64 HOH HOH . E 5 HOH A 88 588 11 HOH HOH . E 5 HOH A 89 589 21 HOH HOH . E 5 HOH A 90 590 33 HOH HOH . E 5 HOH A 91 591 104 HOH HOH . E 5 HOH A 92 592 154 HOH HOH . E 5 HOH A 93 593 57 HOH HOH . E 5 HOH A 94 594 119 HOH HOH . E 5 HOH A 95 595 87 HOH HOH . E 5 HOH A 96 596 142 HOH HOH . E 5 HOH A 97 597 58 HOH HOH . E 5 HOH A 98 598 112 HOH HOH . E 5 HOH A 99 599 17 HOH HOH . E 5 HOH A 100 600 37 HOH HOH . E 5 HOH A 101 601 78 HOH HOH . E 5 HOH A 102 602 5 HOH HOH . E 5 HOH A 103 603 20 HOH HOH . E 5 HOH A 104 604 62 HOH HOH . E 5 HOH A 105 605 199 HOH HOH . E 5 HOH A 106 606 97 HOH HOH . E 5 HOH A 107 607 14 HOH HOH . E 5 HOH A 108 608 74 HOH HOH . E 5 HOH A 109 609 66 HOH HOH . E 5 HOH A 110 610 91 HOH HOH . E 5 HOH A 111 611 111 HOH HOH . E 5 HOH A 112 612 125 HOH HOH . E 5 HOH A 113 613 94 HOH HOH . E 5 HOH A 114 614 218 HOH HOH . E 5 HOH A 115 615 167 HOH HOH . E 5 HOH A 116 616 113 HOH HOH . E 5 HOH A 117 617 53 HOH HOH . E 5 HOH A 118 618 100 HOH HOH . E 5 HOH A 119 619 79 HOH HOH . E 5 HOH A 120 620 157 HOH HOH . E 5 HOH A 121 621 60 HOH HOH . E 5 HOH A 122 622 26 HOH HOH . E 5 HOH A 123 623 145 HOH HOH . E 5 HOH A 124 624 124 HOH HOH . E 5 HOH A 125 625 98 HOH HOH . E 5 HOH A 126 626 161 HOH HOH . E 5 HOH A 127 627 158 HOH HOH . E 5 HOH A 128 628 211 HOH HOH . E 5 HOH A 129 629 69 HOH HOH . E 5 HOH A 130 630 105 HOH HOH . E 5 HOH A 131 631 72 HOH HOH . E 5 HOH A 132 632 110 HOH HOH . E 5 HOH A 133 633 130 HOH HOH . E 5 HOH A 134 634 18 HOH HOH . E 5 HOH A 135 635 144 HOH HOH . E 5 HOH A 136 636 189 HOH HOH . E 5 HOH A 137 637 209 HOH HOH . E 5 HOH A 138 638 138 HOH HOH . E 5 HOH A 139 639 156 HOH HOH . E 5 HOH A 140 640 50 HOH HOH . E 5 HOH A 141 641 179 HOH HOH . E 5 HOH A 142 642 150 HOH HOH . E 5 HOH A 143 643 19 HOH HOH . E 5 HOH A 144 644 184 HOH HOH . E 5 HOH A 145 645 38 HOH HOH . E 5 HOH A 146 646 77 HOH HOH . E 5 HOH A 147 647 22 HOH HOH . E 5 HOH A 148 648 102 HOH HOH . E 5 HOH A 149 649 201 HOH HOH . E 5 HOH A 150 650 181 HOH HOH . E 5 HOH A 151 651 89 HOH HOH . E 5 HOH A 152 652 56 HOH HOH . E 5 HOH A 153 653 133 HOH HOH . E 5 HOH A 154 654 76 HOH HOH . E 5 HOH A 155 655 65 HOH HOH . E 5 HOH A 156 656 29 HOH HOH . E 5 HOH A 157 657 208 HOH HOH . E 5 HOH A 158 658 155 HOH HOH . E 5 HOH A 159 659 149 HOH HOH . E 5 HOH A 160 660 191 HOH HOH . E 5 HOH A 161 661 148 HOH HOH . E 5 HOH A 162 662 81 HOH HOH . E 5 HOH A 163 663 174 HOH HOH . E 5 HOH A 164 664 229 HOH HOH . E 5 HOH A 165 665 101 HOH HOH . E 5 HOH A 166 666 202 HOH HOH . E 5 HOH A 167 667 117 HOH HOH . E 5 HOH A 168 668 183 HOH HOH . E 5 HOH A 169 669 223 HOH HOH . E 5 HOH A 170 670 55 HOH HOH . E 5 HOH A 171 671 203 HOH HOH . E 5 HOH A 172 672 207 HOH HOH . E 5 HOH A 173 673 205 HOH HOH . E 5 HOH A 174 674 39 HOH HOH . E 5 HOH A 175 675 227 HOH HOH . E 5 HOH A 176 676 206 HOH HOH . E 5 HOH A 177 677 225 HOH HOH . E 5 HOH A 178 678 213 HOH HOH . E 5 HOH A 179 679 16 HOH HOH . E 5 HOH A 180 680 88 HOH HOH . E 5 HOH A 181 681 192 HOH HOH . E 5 HOH A 182 682 171 HOH HOH . E 5 HOH A 183 683 131 HOH HOH . E 5 HOH A 184 684 194 HOH HOH . E 5 HOH A 185 685 164 HOH HOH . E 5 HOH A 186 686 114 HOH HOH . E 5 HOH A 187 687 173 HOH HOH . E 5 HOH A 188 688 83 HOH HOH . E 5 HOH A 189 689 166 HOH HOH . E 5 HOH A 190 690 178 HOH HOH . E 5 HOH A 191 691 129 HOH HOH . E 5 HOH A 192 692 196 HOH HOH . E 5 HOH A 193 693 187 HOH HOH . E 5 HOH A 194 694 197 HOH HOH . E 5 HOH A 195 695 226 HOH HOH . E 5 HOH A 196 696 127 HOH HOH . E 5 HOH A 197 697 135 HOH HOH . E 5 HOH A 198 698 122 HOH HOH . E 5 HOH A 199 699 46 HOH HOH . E 5 HOH A 200 700 168 HOH HOH . E 5 HOH A 201 701 217 HOH HOH . E 5 HOH A 202 702 152 HOH HOH . E 5 HOH A 203 703 185 HOH HOH . E 5 HOH A 204 704 215 HOH HOH . E 5 HOH A 205 705 128 HOH HOH . E 5 HOH A 206 706 177 HOH HOH . E 5 HOH A 207 707 116 HOH HOH . E 5 HOH A 208 708 221 HOH HOH . E 5 HOH A 209 709 165 HOH HOH . E 5 HOH A 210 710 163 HOH HOH . E 5 HOH A 211 711 162 HOH HOH . F 5 HOH B 1 101 45 HOH HOH . F 5 HOH B 2 102 8 HOH HOH . F 5 HOH B 3 103 6 HOH HOH . F 5 HOH B 4 104 126 HOH HOH . F 5 HOH B 5 105 216 HOH HOH . F 5 HOH B 6 106 73 HOH HOH . F 5 HOH B 7 107 63 HOH HOH . F 5 HOH B 8 108 123 HOH HOH . F 5 HOH B 9 109 137 HOH HOH . F 5 HOH B 10 110 93 HOH HOH . F 5 HOH B 11 111 230 HOH HOH . F 5 HOH B 12 112 220 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 4 -9.489 15.481 -2.89 1 44.49 ? C1 MPD 402 A 1 HETATM 2 C C2 MPD . . . D 4 -10.1 14.09 -3.064 1 46.05 ? C2 MPD 402 A 1 HETATM 3 O O2 MPD . . . D 4 -9.286 13.187 -2.27 1 43.52 ? O2 MPD 402 A 1 HETATM 4 C CM MPD . . . D 4 -11.528 14.033 -2.512 1 46.9 ? CM MPD 402 A 1 HETATM 5 C C3 MPD . . . D 4 -10.099 13.624 -4.53 1 44.3 ? C3 MPD 402 A 1 HETATM 6 C C4 MPD . . . D 4 -8.699 13.29 -5.072 1 46.16 ? C4 MPD 402 A 1 HETATM 7 O O4 MPD . . . D 4 -8.234 12.096 -4.493 1 48.18 ? O4 MPD 402 A 1 HETATM 8 C C5 MPD . . . D 4 -8.656 13.145 -6.602 1 41.92 ? C5 MPD 402 A 1 HETATM 9 H H11 MPD . . . D 4 -9.173 15.862 -3.861 1 53.39 ? H11 MPD 402 A 1 HETATM 10 H H12 MPD . . . D 4 -10.232 16.152 -2.46 1 53.39 ? H12 MPD 402 A 1 HETATM 11 H H13 MPD . . . D 4 -8.627 15.419 -2.226 1 53.39 ? H13 MPD 402 A 1 HETATM 12 H HO2 MPD . . . D 4 -8.92 12.485 -2.847 1 52.22 ? HO2 MPD 402 A 1 HETATM 13 H HM1 MPD . . . D 4 -12.204 13.677 -3.289 1 56.28 ? HM1 MPD 402 A 1 HETATM 14 H HM2 MPD . . . D 4 -11.562 13.354 -1.66 1 56.28 ? HM2 MPD 402 A 1 HETATM 15 H HM3 MPD . . . D 4 -11.834 15.03 -2.193 1 56.28 ? HM3 MPD 402 A 1 HETATM 16 H H31 MPD . . . D 4 -10.732 12.741 -4.62 1 53.16 ? H31 MPD 402 A 1 HETATM 17 H H32 MPD . . . D 4 -10.54 14.405 -5.149 1 53.16 ? H32 MPD 402 A 1 HETATM 18 H H4 MPD . . . D 4 -8.029 14.104 -4.794 1 55.39 ? H4 MPD 402 A 1 HETATM 19 H HO4 MPD . . . D 4 -7.283 12.188 -4.274 1 57.82 ? HO4 MPD 402 A 1 HETATM 20 H H51 MPD . . . D 4 -8.278 12.157 -6.863 1 50.3 ? H51 MPD 402 A 1 HETATM 21 H H52 MPD . . . D 4 -9.66 13.268 -7.007 1 50.3 ? H52 MPD 402 A 1 HETATM 22 H H53 MPD . . . D 4 -8 13.908 -7.021 1 50.3 ? H53 MPD 402 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #