data_3E86 # _model_server_result.job_id esxLv2AcG-YZfMmjuxvBFg _model_server_result.datetime_utc '2025-09-04 10:54:57' _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 3e86 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 3E86 # _exptl.entry_id 3E86 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 2 _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 3E86 _cell.length_a 68.03 _cell.length_b 68.03 _cell.length_c 89.264 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3E86 _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # 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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,L 1 1,2,3,4 B,H,I,J,K,M 2 1,2,3,4 # 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_445 -x-1,-y-1,z -1 0 0 0 -1 0 0 0 1 -68.03 -68.03 0 3 'crystal symmetry operation' 3_455 -y-1,x,z 0 -1 0 1 0 0 0 0 1 -68.03 0 0 4 'crystal symmetry operation' 4_545 y,-x-1,z 0 1 0 -1 0 0 0 0 1 0 -68.03 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 I 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 metalc ? metalc1 E CA CA . A CA 3 1_555 A O GLY 49 A GLY 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc2 F NA NA . A NA 4 1_555 A O VAL 46 A VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.94 ? metalc ? metalc3 G NA NA . A NA 5 1_555 A OG1 THR 45 A THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc4 G NA NA . A NA 5 1_555 L O HOH . A HOH 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc5 J NA NA . B NA 6 1_555 B OG1 THR 45 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc6 J NA NA . B NA 6 1_555 M O HOH . B HOH 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? # _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 3E86 _atom_sites.fract_transf_matrix[1][1] 0.014699 _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] 0.014699 _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] 0.011203 _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 2 MPD A 1 501 501 MPD MPD . D 3 CS A 1 1 1 CS CS . E 4 CA A 1 3 3 CA CA . F 5 NA A 1 4 4 NA NA . G 5 NA A 1 5 5 NA NA . H 3 CS B 1 2 2 CS CS . I 2 MPD B 1 502 502 MPD MPD . J 5 NA B 1 6 6 NA NA . K 5 NA B 1 7 7 NA NA . L 6 HOH A 1 502 502 HOH HOH . L 6 HOH A 2 503 503 HOH HOH . L 6 HOH A 3 504 504 HOH HOH . L 6 HOH A 4 505 505 HOH HOH . L 6 HOH A 5 506 506 HOH HOH . L 6 HOH A 6 507 507 HOH HOH . L 6 HOH A 7 508 508 HOH HOH . L 6 HOH A 8 509 509 HOH HOH . L 6 HOH A 9 510 510 HOH HOH . L 6 HOH A 10 511 511 HOH HOH . L 6 HOH A 11 512 512 HOH HOH . L 6 HOH A 12 513 513 HOH HOH . L 6 HOH A 13 514 514 HOH HOH . L 6 HOH A 14 515 515 HOH HOH . L 6 HOH A 15 516 516 HOH HOH . L 6 HOH A 16 517 517 HOH HOH . L 6 HOH A 17 518 518 HOH HOH . L 6 HOH A 18 519 519 HOH HOH . L 6 HOH A 19 520 520 HOH HOH . L 6 HOH A 20 521 521 HOH HOH . L 6 HOH A 21 522 522 HOH HOH . L 6 HOH A 22 523 523 HOH HOH . L 6 HOH A 23 524 524 HOH HOH . L 6 HOH A 24 525 525 HOH HOH . L 6 HOH A 25 526 526 HOH HOH . L 6 HOH A 26 527 527 HOH HOH . L 6 HOH A 27 528 528 HOH HOH . L 6 HOH A 28 529 529 HOH HOH . L 6 HOH A 29 530 530 HOH HOH . L 6 HOH A 30 531 531 HOH HOH . L 6 HOH A 31 532 532 HOH HOH . L 6 HOH A 32 533 533 HOH HOH . L 6 HOH A 33 534 534 HOH HOH . L 6 HOH A 34 535 535 HOH HOH . L 6 HOH A 35 536 536 HOH HOH . L 6 HOH A 36 537 537 HOH HOH . L 6 HOH A 37 538 538 HOH HOH . L 6 HOH A 38 539 539 HOH HOH . L 6 HOH A 39 540 540 HOH HOH . L 6 HOH A 40 541 541 HOH HOH . L 6 HOH A 41 542 542 HOH HOH . L 6 HOH A 42 543 543 HOH HOH . L 6 HOH A 43 544 544 HOH HOH . L 6 HOH A 44 545 545 HOH HOH . L 6 HOH A 45 546 546 HOH HOH . L 6 HOH A 46 547 547 HOH HOH . L 6 HOH A 47 548 548 HOH HOH . L 6 HOH A 48 549 549 HOH HOH . L 6 HOH A 49 550 550 HOH HOH . L 6 HOH A 50 551 551 HOH HOH . L 6 HOH A 51 552 552 HOH HOH . L 6 HOH A 52 553 553 HOH HOH . L 6 HOH A 53 554 554 HOH HOH . L 6 HOH A 54 555 555 HOH HOH . L 6 HOH A 55 556 556 HOH HOH . L 6 HOH A 56 557 557 HOH HOH . L 6 HOH A 57 558 558 HOH HOH . L 6 HOH A 58 559 559 HOH HOH . L 6 HOH A 59 560 560 HOH HOH . L 6 HOH A 60 561 561 HOH HOH . L 6 HOH A 61 562 562 HOH HOH . L 6 HOH A 62 563 563 HOH HOH . L 6 HOH A 63 564 564 HOH HOH . L 6 HOH A 64 565 565 HOH HOH . L 6 HOH A 65 566 566 HOH HOH . L 6 HOH A 66 567 567 HOH HOH . L 6 HOH A 67 568 568 HOH HOH . L 6 HOH A 68 569 569 HOH HOH . L 6 HOH A 69 570 570 HOH HOH . L 6 HOH A 70 571 571 HOH HOH . L 6 HOH A 71 572 572 HOH HOH . L 6 HOH A 72 573 573 HOH HOH . L 6 HOH A 73 574 574 HOH HOH . L 6 HOH A 74 575 575 HOH HOH . L 6 HOH A 75 576 576 HOH HOH . L 6 HOH A 76 577 577 HOH HOH . L 6 HOH A 77 578 578 HOH HOH . L 6 HOH A 78 579 579 HOH HOH . L 6 HOH A 79 580 580 HOH HOH . L 6 HOH A 80 581 581 HOH HOH . L 6 HOH A 81 582 582 HOH HOH . L 6 HOH A 82 583 545 HOH HOH . M 6 HOH B 1 544 544 HOH HOH . M 6 HOH B 2 546 546 HOH HOH . M 6 HOH B 3 547 547 HOH HOH . M 6 HOH B 4 548 548 HOH HOH . M 6 HOH B 5 549 549 HOH HOH . M 6 HOH B 6 550 550 HOH HOH . M 6 HOH B 7 551 551 HOH HOH . M 6 HOH B 8 552 552 HOH HOH . M 6 HOH B 9 553 553 HOH HOH . M 6 HOH B 10 554 554 HOH HOH . M 6 HOH B 11 555 555 HOH HOH . M 6 HOH B 12 556 556 HOH HOH . M 6 HOH B 13 557 557 HOH HOH . M 6 HOH B 14 558 558 HOH HOH . M 6 HOH B 15 559 559 HOH HOH . M 6 HOH B 16 560 560 HOH HOH . M 6 HOH B 17 561 561 HOH HOH . M 6 HOH B 18 562 562 HOH HOH . M 6 HOH B 19 563 563 HOH HOH . M 6 HOH B 20 564 564 HOH HOH . M 6 HOH B 21 565 565 HOH HOH . M 6 HOH B 22 566 566 HOH HOH . M 6 HOH B 23 567 567 HOH HOH . M 6 HOH B 24 568 568 HOH HOH . M 6 HOH B 25 569 569 HOH HOH . M 6 HOH B 26 570 570 HOH HOH . M 6 HOH B 27 571 571 HOH HOH . M 6 HOH B 28 572 572 HOH HOH . M 6 HOH B 29 573 573 HOH HOH . M 6 HOH B 30 574 574 HOH HOH . M 6 HOH B 31 575 575 HOH HOH . M 6 HOH B 32 576 576 HOH HOH . M 6 HOH B 33 577 577 HOH HOH . M 6 HOH B 34 578 578 HOH HOH . M 6 HOH B 35 579 579 HOH HOH . M 6 HOH B 36 580 580 HOH HOH . M 6 HOH B 37 581 581 HOH HOH . M 6 HOH B 38 582 582 HOH HOH . M 6 HOH B 39 583 583 HOH HOH . M 6 HOH B 40 584 584 HOH HOH . M 6 HOH B 41 585 585 HOH HOH . M 6 HOH B 42 586 586 HOH HOH . M 6 HOH B 43 587 587 HOH HOH . M 6 HOH B 44 588 588 HOH HOH . M 6 HOH B 45 589 589 HOH HOH . M 6 HOH B 46 590 590 HOH HOH . M 6 HOH B 47 591 591 HOH HOH . M 6 HOH B 48 592 592 HOH HOH . M 6 HOH B 49 593 593 HOH HOH . M 6 HOH B 50 594 594 HOH HOH . M 6 HOH B 51 595 595 HOH HOH . M 6 HOH B 52 596 596 HOH HOH . M 6 HOH B 53 597 597 HOH HOH . M 6 HOH B 54 598 598 HOH HOH . M 6 HOH B 55 599 599 HOH HOH . M 6 HOH B 56 600 600 HOH HOH . M 6 HOH B 57 601 601 HOH HOH . M 6 HOH B 58 602 602 HOH HOH . M 6 HOH B 59 603 603 HOH HOH . M 6 HOH B 60 604 604 HOH HOH . M 6 HOH B 61 605 605 HOH HOH . M 6 HOH B 62 606 606 HOH HOH . M 6 HOH B 63 607 607 HOH HOH . M 6 HOH B 64 608 608 HOH HOH . M 6 HOH B 65 609 609 HOH HOH . M 6 HOH B 66 610 610 HOH HOH . M 6 HOH B 67 611 611 HOH HOH . M 6 HOH B 68 612 612 HOH HOH . M 6 HOH B 69 613 613 HOH HOH . M 6 HOH B 70 614 614 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 . . . C 2 -23.021 -33.86 10.188 1 39.07 ? C1 MPD 501 A 1 HETATM 2 C C2 MPD . . . C 2 -23.295 -34.839 11.334 1 44.65 ? C2 MPD 501 A 1 HETATM 3 O O2 MPD . . . C 2 -24.68 -34.791 11.682 1 37.86 ? O2 MPD 501 A 1 HETATM 4 C CM MPD . . . C 2 -22.922 -36.253 10.895 1 39.01 ? CM MPD 501 A 1 HETATM 5 C C3 MPD . . . C 2 -22.456 -34.446 12.556 1 43.82 ? C3 MPD 501 A 1 HETATM 6 C C4 MPD . . . C 2 -22.92 -33.614 13.749 1 46.32 ? C4 MPD 501 A 1 HETATM 7 O O4 MPD . . . C 2 -24.12 -34.173 14.291 1 49.42 ? O4 MPD 501 A 1 HETATM 8 C C5 MPD . . . C 2 -21.828 -33.588 14.82 1 47.35 ? C5 MPD 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #