data_5N3F # _model_server_result.job_id L4hqyeQQuIKFDsTIjLx_QQ _model_server_result.datetime_utc '2025-01-10 08:18:29' _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 5n3f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 5N3F # _exptl.entry_id 5N3F _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 5N3F _cell.length_a 58.765 _cell.length_b 72.194 _cell.length_c 108.76 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5N3F _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 software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 # 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C SEP 13 A SEP 10 1_555 A N GLU 14 A GLU 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C PHE 141 A PHE 138 1_555 A N SEP 142 A SEP 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale4 A C SEP 142 A SEP 139 1_555 A N GLU 143 A GLU 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale5 A C TRP 199 A TRP 196 1_555 A N TPO 200 A TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale6 A C TPO 200 A TPO 197 1_555 A N LEU 201 A LEU 198 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 261 n n C1 H11 MPD sing 262 n n C1 H12 MPD sing 263 n n C1 H13 MPD sing 264 n n C2 O2 MPD sing 265 n n C2 CM MPD sing 266 n n C2 C3 MPD sing 267 n n O2 HO2 MPD sing 268 n n CM HM1 MPD sing 269 n n CM HM2 MPD sing 270 n n CM HM3 MPD sing 271 n n C3 C4 MPD sing 272 n n C3 H31 MPD sing 273 n n C3 H32 MPD sing 274 n n C4 O4 MPD sing 275 n n C4 C5 MPD sing 276 n n C4 H4 MPD sing 277 n n O4 HO4 MPD sing 278 n n C5 H51 MPD sing 279 n n C5 H52 MPD sing 280 n n C5 H53 MPD sing 281 n n # _atom_sites.entry_id 5N3F _atom_sites.fract_transf_matrix[1][1] 0.017017 _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] 0.013852 _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] 0.009195 _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 MPD A 1 401 1 MPD MPD . D 3 MPD A 1 402 2 MPD MPD . E 4 463 A 1 403 1 463 XXX . F 4 463 A 1 404 2 463 XXX . G 5 HOH A 1 501 132 HOH HOH . G 5 HOH A 2 502 216 HOH HOH . G 5 HOH A 3 503 178 HOH HOH . G 5 HOH A 4 504 191 HOH HOH . G 5 HOH A 5 505 247 HOH HOH . G 5 HOH A 6 506 252 HOH HOH . G 5 HOH A 7 507 161 HOH HOH . G 5 HOH A 8 508 151 HOH HOH . G 5 HOH A 9 509 159 HOH HOH . G 5 HOH A 10 510 135 HOH HOH . G 5 HOH A 11 511 77 HOH HOH . G 5 HOH A 12 512 52 HOH HOH . G 5 HOH A 13 513 123 HOH HOH . G 5 HOH A 14 514 165 HOH HOH . G 5 HOH A 15 515 148 HOH HOH . G 5 HOH A 16 516 130 HOH HOH . G 5 HOH A 17 517 83 HOH HOH . G 5 HOH A 18 518 53 HOH HOH . G 5 HOH A 19 519 73 HOH HOH . G 5 HOH A 20 520 168 HOH HOH . G 5 HOH A 21 521 99 HOH HOH . G 5 HOH A 22 522 54 HOH HOH . G 5 HOH A 23 523 212 HOH HOH . G 5 HOH A 24 524 177 HOH HOH . G 5 HOH A 25 525 124 HOH HOH . G 5 HOH A 26 526 58 HOH HOH . G 5 HOH A 27 527 64 HOH HOH . G 5 HOH A 28 528 236 HOH HOH . G 5 HOH A 29 529 62 HOH HOH . G 5 HOH A 30 530 185 HOH HOH . G 5 HOH A 31 531 213 HOH HOH . G 5 HOH A 32 532 246 HOH HOH . G 5 HOH A 33 533 65 HOH HOH . G 5 HOH A 34 534 144 HOH HOH . G 5 HOH A 35 535 50 HOH HOH . G 5 HOH A 36 536 140 HOH HOH . G 5 HOH A 37 537 79 HOH HOH . G 5 HOH A 38 538 162 HOH HOH . G 5 HOH A 39 539 9 HOH HOH . G 5 HOH A 40 540 121 HOH HOH . G 5 HOH A 41 541 81 HOH HOH . G 5 HOH A 42 542 223 HOH HOH . G 5 HOH A 43 543 192 HOH HOH . G 5 HOH A 44 544 166 HOH HOH . G 5 HOH A 45 545 103 HOH HOH . G 5 HOH A 46 546 42 HOH HOH . G 5 HOH A 47 547 104 HOH HOH . G 5 HOH A 48 548 70 HOH HOH . G 5 HOH A 49 549 40 HOH HOH . G 5 HOH A 50 550 23 HOH HOH . G 5 HOH A 51 551 63 HOH HOH . G 5 HOH A 52 552 117 HOH HOH . G 5 HOH A 53 553 249 HOH HOH . G 5 HOH A 54 554 71 HOH HOH . G 5 HOH A 55 555 27 HOH HOH . G 5 HOH A 56 556 7 HOH HOH . G 5 HOH A 57 557 112 HOH HOH . G 5 HOH A 58 558 90 HOH HOH . G 5 HOH A 59 559 22 HOH HOH . G 5 HOH A 60 560 11 HOH HOH . G 5 HOH A 61 561 6 HOH HOH . G 5 HOH A 62 562 60 HOH HOH . G 5 HOH A 63 563 85 HOH HOH . G 5 HOH A 64 564 147 HOH HOH . G 5 HOH A 65 565 149 HOH HOH . G 5 HOH A 66 566 80 HOH HOH . G 5 HOH A 67 567 243 HOH HOH . G 5 HOH A 68 568 47 HOH HOH . G 5 HOH A 69 569 189 HOH HOH . G 5 HOH A 70 570 51 HOH HOH . G 5 HOH A 71 571 150 HOH HOH . G 5 HOH A 72 572 24 HOH HOH . G 5 HOH A 73 573 107 HOH HOH . G 5 HOH A 74 574 28 HOH HOH . G 5 HOH A 75 575 110 HOH HOH . G 5 HOH A 76 576 229 HOH HOH . G 5 HOH A 77 577 86 HOH HOH . G 5 HOH A 78 578 10 HOH HOH . G 5 HOH A 79 579 203 HOH HOH . G 5 HOH A 80 580 194 HOH HOH . G 5 HOH A 81 581 221 HOH HOH . G 5 HOH A 82 582 21 HOH HOH . G 5 HOH A 83 583 16 HOH HOH . G 5 HOH A 84 584 29 HOH HOH . G 5 HOH A 85 585 152 HOH HOH . G 5 HOH A 86 586 69 HOH HOH . G 5 HOH A 87 587 25 HOH HOH . G 5 HOH A 88 588 3 HOH HOH . G 5 HOH A 89 589 138 HOH HOH . G 5 HOH A 90 590 55 HOH HOH . G 5 HOH A 91 591 43 HOH HOH . G 5 HOH A 92 592 91 HOH HOH . G 5 HOH A 93 593 227 HOH HOH . G 5 HOH A 94 594 222 HOH HOH . G 5 HOH A 95 595 93 HOH HOH . G 5 HOH A 96 596 35 HOH HOH . G 5 HOH A 97 597 2 HOH HOH . G 5 HOH A 98 598 20 HOH HOH . G 5 HOH A 99 599 26 HOH HOH . G 5 HOH A 100 600 134 HOH HOH . G 5 HOH A 101 601 251 HOH HOH . G 5 HOH A 102 602 101 HOH HOH . G 5 HOH A 103 603 88 HOH HOH . G 5 HOH A 104 604 76 HOH HOH . G 5 HOH A 105 605 234 HOH HOH . G 5 HOH A 106 606 67 HOH HOH . G 5 HOH A 107 607 30 HOH HOH . G 5 HOH A 108 608 114 HOH HOH . G 5 HOH A 109 609 92 HOH HOH . G 5 HOH A 110 610 153 HOH HOH . G 5 HOH A 111 611 231 HOH HOH . G 5 HOH A 112 612 46 HOH HOH . G 5 HOH A 113 613 32 HOH HOH . G 5 HOH A 114 614 233 HOH HOH . G 5 HOH A 115 615 18 HOH HOH . G 5 HOH A 116 616 154 HOH HOH . G 5 HOH A 117 617 199 HOH HOH . G 5 HOH A 118 618 38 HOH HOH . G 5 HOH A 119 619 228 HOH HOH . G 5 HOH A 120 620 224 HOH HOH . G 5 HOH A 121 621 12 HOH HOH . G 5 HOH A 122 622 141 HOH HOH . G 5 HOH A 123 623 186 HOH HOH . G 5 HOH A 124 624 56 HOH HOH . G 5 HOH A 125 625 193 HOH HOH . G 5 HOH A 126 626 254 HOH HOH . G 5 HOH A 127 627 115 HOH HOH . G 5 HOH A 128 628 19 HOH HOH . G 5 HOH A 129 629 102 HOH HOH . G 5 HOH A 130 630 136 HOH HOH . G 5 HOH A 131 631 49 HOH HOH . G 5 HOH A 132 632 14 HOH HOH . G 5 HOH A 133 633 204 HOH HOH . G 5 HOH A 134 634 100 HOH HOH . G 5 HOH A 135 635 226 HOH HOH . G 5 HOH A 136 636 146 HOH HOH . G 5 HOH A 137 637 158 HOH HOH . G 5 HOH A 138 638 210 HOH HOH . G 5 HOH A 139 639 116 HOH HOH . G 5 HOH A 140 640 111 HOH HOH . G 5 HOH A 141 641 68 HOH HOH . G 5 HOH A 142 642 137 HOH HOH . G 5 HOH A 143 643 41 HOH HOH . G 5 HOH A 144 644 44 HOH HOH . G 5 HOH A 145 645 45 HOH HOH . G 5 HOH A 146 646 230 HOH HOH . G 5 HOH A 147 647 98 HOH HOH . G 5 HOH A 148 648 108 HOH HOH . G 5 HOH A 149 649 72 HOH HOH . G 5 HOH A 150 650 239 HOH HOH . G 5 HOH A 151 651 57 HOH HOH . G 5 HOH A 152 652 96 HOH HOH . G 5 HOH A 153 653 188 HOH HOH . G 5 HOH A 154 654 31 HOH HOH . G 5 HOH A 155 655 33 HOH HOH . G 5 HOH A 156 656 174 HOH HOH . G 5 HOH A 157 657 170 HOH HOH . G 5 HOH A 158 658 48 HOH HOH . G 5 HOH A 159 659 8 HOH HOH . G 5 HOH A 160 660 217 HOH HOH . G 5 HOH A 161 661 238 HOH HOH . G 5 HOH A 162 662 84 HOH HOH . G 5 HOH A 163 663 61 HOH HOH . G 5 HOH A 164 664 179 HOH HOH . G 5 HOH A 165 665 172 HOH HOH . G 5 HOH A 166 666 176 HOH HOH . G 5 HOH A 167 667 250 HOH HOH . G 5 HOH A 168 668 200 HOH HOH . G 5 HOH A 169 669 66 HOH HOH . G 5 HOH A 170 670 17 HOH HOH . G 5 HOH A 171 671 36 HOH HOH . G 5 HOH A 172 672 37 HOH HOH . G 5 HOH A 173 673 175 HOH HOH . G 5 HOH A 174 674 106 HOH HOH . G 5 HOH A 175 675 127 HOH HOH . G 5 HOH A 176 676 240 HOH HOH . G 5 HOH A 177 677 218 HOH HOH . G 5 HOH A 178 678 59 HOH HOH . G 5 HOH A 179 679 183 HOH HOH . G 5 HOH A 180 680 105 HOH HOH . G 5 HOH A 181 681 206 HOH HOH . G 5 HOH A 182 682 34 HOH HOH . G 5 HOH A 183 683 225 HOH HOH . G 5 HOH A 184 684 248 HOH HOH . G 5 HOH A 185 685 211 HOH HOH . G 5 HOH A 186 686 74 HOH HOH . G 5 HOH A 187 687 187 HOH HOH . G 5 HOH A 188 688 253 HOH HOH . G 5 HOH A 189 689 197 HOH HOH . G 5 HOH A 190 690 180 HOH HOH . G 5 HOH A 191 691 235 HOH HOH . G 5 HOH A 192 692 241 HOH HOH . G 5 HOH A 193 693 39 HOH HOH . G 5 HOH A 194 694 118 HOH HOH . G 5 HOH A 195 695 208 HOH HOH . G 5 HOH A 196 696 173 HOH HOH . G 5 HOH A 197 697 171 HOH HOH . G 5 HOH A 198 698 207 HOH HOH . G 5 HOH A 199 699 182 HOH HOH . G 5 HOH A 200 700 75 HOH HOH . G 5 HOH A 201 701 245 HOH HOH . G 5 HOH A 202 702 145 HOH HOH . G 5 HOH A 203 703 219 HOH HOH . G 5 HOH A 204 704 202 HOH HOH . G 5 HOH A 205 705 255 HOH HOH . G 5 HOH A 206 706 125 HOH HOH . G 5 HOH A 207 707 155 HOH HOH . G 5 HOH A 208 708 220 HOH HOH . G 5 HOH A 209 709 215 HOH HOH . G 5 HOH A 210 710 163 HOH HOH . G 5 HOH A 211 711 89 HOH HOH . G 5 HOH A 212 712 164 HOH HOH . G 5 HOH A 213 713 198 HOH HOH . G 5 HOH A 214 714 190 HOH HOH . G 5 HOH A 215 715 133 HOH HOH . G 5 HOH A 216 716 244 HOH HOH . G 5 HOH A 217 717 94 HOH HOH . G 5 HOH A 218 718 237 HOH HOH . G 5 HOH A 219 719 142 HOH HOH . G 5 HOH A 220 720 131 HOH HOH . G 5 HOH A 221 721 169 HOH HOH . G 5 HOH A 222 722 196 HOH HOH . G 5 HOH A 223 723 201 HOH HOH . G 5 HOH A 224 724 97 HOH HOH . H 5 HOH B 1 101 82 HOH HOH . H 5 HOH B 2 102 15 HOH HOH . H 5 HOH B 3 103 13 HOH HOH . H 5 HOH B 4 104 4 HOH HOH . H 5 HOH B 5 105 5 HOH HOH . H 5 HOH B 6 106 232 HOH HOH . H 5 HOH B 7 107 214 HOH HOH . H 5 HOH B 8 108 119 HOH HOH . H 5 HOH B 9 109 122 HOH HOH . H 5 HOH B 10 110 157 HOH HOH . H 5 HOH B 11 111 160 HOH HOH . H 5 HOH B 12 112 78 HOH HOH . H 5 HOH B 13 113 139 HOH HOH . H 5 HOH B 14 114 181 HOH HOH . H 5 HOH B 15 115 209 HOH HOH . H 5 HOH B 16 116 242 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 11.122 1.932 -16.034 0.72 32.58 ? C1 MPD 402 A 1 HETATM 2 C C2 MPD . . . D 3 10.112 1.419 -17.063 0.72 32.91 ? C2 MPD 402 A 1 HETATM 3 O O2 MPD . . . D 3 9.983 2.41 -18.11 0.72 31.52 ? O2 MPD 402 A 1 HETATM 4 C CM MPD . . . D 3 10.593 0.118 -17.728 0.72 26.09 ? CM MPD 402 A 1 HETATM 5 C C3 MPD . . . D 3 8.752 1.167 -16.433 0.72 32.6 ? C3 MPD 402 A 1 HETATM 6 C C4 MPD . . . D 3 8.193 2.347 -15.62 0.72 36.37 ? C4 MPD 402 A 1 HETATM 7 O O4 MPD . . . D 3 7.826 3.417 -16.466 0.72 29.37 ? O4 MPD 402 A 1 HETATM 8 C C5 MPD . . . D 3 6.94 1.881 -14.881 0.72 34.55 ? C5 MPD 402 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 8 #