data_5VEP # _model_server_result.job_id F58Yxps0c9IEV4yfJQ_GUg _model_server_result.datetime_utc '2024-11-02 05:28:45' _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 5vep # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":503}' # _entry.id 5VEP # _exptl.entry_id 5VEP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 6 _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 5VEP _cell.length_a 91.82 _cell.length_b 91.82 _cell.length_c 233.649 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VEP _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 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 dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 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,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 2 1,2 # 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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 116.8245 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 F N N ? 4 G N N ? 4 H N N ? 4 N N N ? 4 O 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 239 A GLY 280 1_555 A N LLP 240 A LLP 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale2 A C LLP 240 A LLP 281 1_555 A N THR 241 A THR 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale3 B C GLY 239 B GLY 280 1_555 B N LLP 240 B LLP 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 B C LLP 240 B LLP 281 1_555 B N THR 241 B THR 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 A OE1 GLU 6 A GLU 47 1_555 K CA CA . A CA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? metalc ? metalc2 A OE2 GLU 6 A GLU 47 1_555 K CA CA . A CA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc3 A OE1 GLN 81 A GLN 122 1_555 I CA CA . A CA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc4 A OE1 GLN 81 A GLN 122 1_555 I CA CA . A CA 507 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc5 A O HIS 199 A HIS 240 1_555 J CA CA . A CA 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc6 I CA CA . A CA 507 1_555 Q O HOH . A HOH 645 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc7 I CA CA . A CA 507 1_555 Q O HOH . A HOH 645 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc8 I CA CA . A CA 507 1_555 Q O HOH . A HOH 659 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.049 ? metalc ? metalc9 I CA CA . A CA 507 1_555 Q O HOH . A HOH 672 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc10 I CA CA . A CA 507 1_555 Q O HOH . A HOH 672 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc11 J CA CA . A CA 508 1_555 Q O HOH . A HOH 622 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.003 ? metalc ? metalc12 J CA CA . A CA 508 1_555 Q O HOH . A HOH 664 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? metalc ? metalc13 J CA CA . A CA 508 1_555 Q O HOH . A HOH 665 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.857 ? metalc ? metalc14 J CA CA . A CA 508 1_555 Q O HOH . A HOH 668 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.99 ? metalc ? metalc15 K CA CA . A CA 509 1_555 Q O HOH . A HOH 602 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc16 K CA CA . A CA 509 1_555 Q O HOH . A HOH 612 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? metalc ? metalc17 K CA CA . A CA 509 1_555 Q O HOH . A HOH 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.137 ? metalc ? metalc18 B O HIS 199 B HIS 240 1_555 P CA CA . B CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc19 P CA CA . B CA 505 1_555 R O HOH . B HOH 639 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc20 P CA CA . B CA 505 1_555 R O HOH . B HOH 647 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.801 ? metalc ? metalc21 P CA CA . B CA 505 1_555 R O HOH . B HOH 668 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc22 P CA CA . B CA 505 1_555 R O HOH . B HOH 673 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc23 P CA CA . B CA 505 1_555 R O HOH . B HOH 687 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # _atom_sites.entry_id 5VEP _atom_sites.fract_transf_matrix[1][1] 0.010891 _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] 0.010891 _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] 0.00428 _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 EPE A 1 501 457 EPE EPE . D 3 PEG A 1 502 458 PEG PEG . E 4 GOL A 1 503 459 GOL GOL . F 4 GOL A 1 504 460 GOL GOL . G 4 GOL A 1 505 461 GOL GOL . H 4 GOL A 1 506 462 GOL GOL . I 5 CA A 1 507 471 CA CA . J 5 CA A 1 508 472 CA CA . K 5 CA A 1 509 473 CA CA . L 2 EPE B 1 501 457 EPE EPE . M 3 PEG B 1 502 458 PEG PEG . N 4 GOL B 1 503 459 GOL GOL . O 4 GOL B 1 504 460 GOL GOL . P 5 CA B 1 505 471 CA CA . Q 6 HOH A 1 601 625 HOH HOH . Q 6 HOH A 2 602 508 HOH HOH . Q 6 HOH A 3 603 583 HOH HOH . Q 6 HOH A 4 604 601 HOH HOH . Q 6 HOH A 5 605 598 HOH HOH . Q 6 HOH A 6 606 593 HOH HOH . Q 6 HOH A 7 607 582 HOH HOH . Q 6 HOH A 8 608 586 HOH HOH . Q 6 HOH A 9 609 592 HOH HOH . Q 6 HOH A 10 610 572 HOH HOH . Q 6 HOH A 11 611 619 HOH HOH . Q 6 HOH A 12 612 512 HOH HOH . Q 6 HOH A 13 613 606 HOH HOH . Q 6 HOH A 14 614 597 HOH HOH . Q 6 HOH A 15 615 610 HOH HOH . Q 6 HOH A 16 616 615 HOH HOH . Q 6 HOH A 17 617 596 HOH HOH . Q 6 HOH A 18 618 604 HOH HOH . Q 6 HOH A 19 619 594 HOH HOH . Q 6 HOH A 20 620 569 HOH HOH . Q 6 HOH A 21 621 578 HOH HOH . Q 6 HOH A 22 622 506 HOH HOH . Q 6 HOH A 23 623 584 HOH HOH . Q 6 HOH A 24 624 588 HOH HOH . Q 6 HOH A 25 625 580 HOH HOH . Q 6 HOH A 26 626 616 HOH HOH . Q 6 HOH A 27 627 563 HOH HOH . Q 6 HOH A 28 628 571 HOH HOH . Q 6 HOH A 29 629 581 HOH HOH . Q 6 HOH A 30 630 576 HOH HOH . Q 6 HOH A 31 631 595 HOH HOH . Q 6 HOH A 32 632 613 HOH HOH . Q 6 HOH A 33 633 591 HOH HOH . Q 6 HOH A 34 634 600 HOH HOH . Q 6 HOH A 35 635 589 HOH HOH . Q 6 HOH A 36 636 607 HOH HOH . Q 6 HOH A 37 637 590 HOH HOH . Q 6 HOH A 38 638 623 HOH HOH . Q 6 HOH A 39 639 611 HOH HOH . Q 6 HOH A 40 640 574 HOH HOH . Q 6 HOH A 41 641 622 HOH HOH . Q 6 HOH A 42 642 621 HOH HOH . Q 6 HOH A 43 643 609 HOH HOH . Q 6 HOH A 44 644 564 HOH HOH . Q 6 HOH A 45 645 502 HOH HOH . Q 6 HOH A 46 646 617 HOH HOH . Q 6 HOH A 47 647 573 HOH HOH . Q 6 HOH A 48 648 577 HOH HOH . Q 6 HOH A 49 649 602 HOH HOH . Q 6 HOH A 50 650 575 HOH HOH . Q 6 HOH A 51 651 612 HOH HOH . Q 6 HOH A 52 652 579 HOH HOH . Q 6 HOH A 53 653 620 HOH HOH . Q 6 HOH A 54 654 608 HOH HOH . Q 6 HOH A 55 655 587 HOH HOH . Q 6 HOH A 56 656 565 HOH HOH . Q 6 HOH A 57 657 566 HOH HOH . Q 6 HOH A 58 658 567 HOH HOH . Q 6 HOH A 59 659 503 HOH HOH . Q 6 HOH A 60 660 568 HOH HOH . Q 6 HOH A 61 661 605 HOH HOH . Q 6 HOH A 62 662 509 HOH HOH . Q 6 HOH A 63 663 603 HOH HOH . Q 6 HOH A 64 664 505 HOH HOH . Q 6 HOH A 65 665 507 HOH HOH . Q 6 HOH A 66 666 570 HOH HOH . Q 6 HOH A 67 667 587 HOH HOH . Q 6 HOH A 68 668 504 HOH HOH . Q 6 HOH A 69 669 599 HOH HOH . Q 6 HOH A 70 670 624 HOH HOH . Q 6 HOH A 71 671 510 HOH HOH . Q 6 HOH A 72 672 501 HOH HOH . R 6 HOH B 1 601 638 HOH HOH . R 6 HOH B 2 602 627 HOH HOH . R 6 HOH B 3 603 585 HOH HOH . R 6 HOH B 4 604 594 HOH HOH . R 6 HOH B 5 605 511 HOH HOH . R 6 HOH B 6 606 584 HOH HOH . R 6 HOH B 7 607 577 HOH HOH . R 6 HOH B 8 608 601 HOH HOH . R 6 HOH B 9 609 630 HOH HOH . R 6 HOH B 10 610 575 HOH HOH . R 6 HOH B 11 611 615 HOH HOH . R 6 HOH B 12 612 564 HOH HOH . R 6 HOH B 13 613 596 HOH HOH . R 6 HOH B 14 614 603 HOH HOH . R 6 HOH B 15 615 632 HOH HOH . R 6 HOH B 16 616 588 HOH HOH . R 6 HOH B 17 617 633 HOH HOH . R 6 HOH B 18 618 609 HOH HOH . R 6 HOH B 19 619 604 HOH HOH . R 6 HOH B 20 620 613 HOH HOH . R 6 HOH B 21 621 635 HOH HOH . R 6 HOH B 22 622 599 HOH HOH . R 6 HOH B 23 623 574 HOH HOH . R 6 HOH B 24 624 621 HOH HOH . R 6 HOH B 25 625 597 HOH HOH . R 6 HOH B 26 626 610 HOH HOH . R 6 HOH B 27 627 628 HOH HOH . R 6 HOH B 28 628 565 HOH HOH . R 6 HOH B 29 629 585 HOH HOH . R 6 HOH B 30 630 598 HOH HOH . R 6 HOH B 31 631 626 HOH HOH . R 6 HOH B 32 632 619 HOH HOH . R 6 HOH B 33 633 634 HOH HOH . R 6 HOH B 34 634 617 HOH HOH . R 6 HOH B 35 635 567 HOH HOH . R 6 HOH B 36 636 579 HOH HOH . R 6 HOH B 37 637 571 HOH HOH . R 6 HOH B 38 638 591 HOH HOH . R 6 HOH B 39 639 503 HOH HOH . R 6 HOH B 40 640 589 HOH HOH . R 6 HOH B 41 641 595 HOH HOH . R 6 HOH B 42 642 622 HOH HOH . R 6 HOH B 43 643 593 HOH HOH . R 6 HOH B 44 644 625 HOH HOH . R 6 HOH B 45 645 624 HOH HOH . R 6 HOH B 46 646 636 HOH HOH . R 6 HOH B 47 647 504 HOH HOH . R 6 HOH B 48 648 592 HOH HOH . R 6 HOH B 49 649 606 HOH HOH . R 6 HOH B 50 650 563 HOH HOH . R 6 HOH B 51 651 581 HOH HOH . R 6 HOH B 52 652 620 HOH HOH . R 6 HOH B 53 653 614 HOH HOH . R 6 HOH B 54 654 580 HOH HOH . R 6 HOH B 55 655 569 HOH HOH . R 6 HOH B 56 656 612 HOH HOH . R 6 HOH B 57 657 568 HOH HOH . R 6 HOH B 58 658 616 HOH HOH . R 6 HOH B 59 659 637 HOH HOH . R 6 HOH B 60 660 607 HOH HOH . R 6 HOH B 61 661 590 HOH HOH . R 6 HOH B 62 662 602 HOH HOH . R 6 HOH B 63 663 626 HOH HOH . R 6 HOH B 64 664 631 HOH HOH . R 6 HOH B 65 665 566 HOH HOH . R 6 HOH B 66 666 611 HOH HOH . R 6 HOH B 67 667 573 HOH HOH . R 6 HOH B 68 668 502 HOH HOH . R 6 HOH B 69 669 562 HOH HOH . R 6 HOH B 70 670 582 HOH HOH . R 6 HOH B 71 671 586 HOH HOH . R 6 HOH B 72 672 600 HOH HOH . R 6 HOH B 73 673 501 HOH HOH . R 6 HOH B 74 674 605 HOH HOH . R 6 HOH B 75 675 623 HOH HOH . R 6 HOH B 76 676 576 HOH HOH . R 6 HOH B 77 677 572 HOH HOH . R 6 HOH B 78 678 561 HOH HOH . R 6 HOH B 79 679 618 HOH HOH . R 6 HOH B 80 680 608 HOH HOH . R 6 HOH B 81 681 629 HOH HOH . R 6 HOH B 82 682 560 HOH HOH . R 6 HOH B 83 683 583 HOH HOH . R 6 HOH B 84 684 578 HOH HOH . R 6 HOH B 85 685 641 HOH HOH . R 6 HOH B 86 686 639 HOH HOH . R 6 HOH B 87 687 505 HOH HOH . R 6 HOH B 88 688 570 HOH HOH . R 6 HOH B 89 689 642 HOH HOH . R 6 HOH B 90 690 640 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 GOL . . . N 4 47.398 38.85 57.332 1 51.13 ? C1 GOL 503 B 1 HETATM 2 O O1 GOL . . . N 4 47.541 37.807 56.349 1 51.28 ? O1 GOL 503 B 1 HETATM 3 C C2 GOL . . . N 4 46.28 38.459 58.304 1 50.37 ? C2 GOL 503 B 1 HETATM 4 O O2 GOL . . . N 4 46.092 37.034 58.304 1 50.4 ? O2 GOL 503 B 1 HETATM 5 C C3 GOL . . . N 4 44.971 39.122 57.897 1 49.69 ? C3 GOL 503 B 1 HETATM 6 O O3 GOL . . . N 4 43.899 38.171 57.969 1 48.46 ? O3 GOL 503 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 236 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #