data_5LGD # _model_server_result.job_id Ouhb92YV3bmZteOF_Y6x7Q _model_server_result.datetime_utc '2024-10-28 02:35:57' _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 5lgd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":516}' # _entry.id 5LGD # _exptl.entry_id 5LGD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 114.85 _cell.angle_gamma 90 _cell.entry_id 5LGD _cell.length_a 129.826 _cell.length_b 40.726 _cell.length_c 138.836 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LGD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V _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 ? 6 N N N ? 6 O N N ? 6 P N N ? 6 Q N N ? 6 S N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 MAN NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 C 1 NAG A 458 NAG 3 n C NAG 2 C 2 NAG A 459 NAG 3 n C MAN 3 C 3 MAN A 468 MAN # 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 disulf ? disulf1 A SG CYS 243 A CYS 243 1_555 A SG CYS 311 A CYS 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 A SG CYS 272 A CYS 272 1_555 A SG CYS 333 A CYS 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? disulf ? disulf3 A SG CYS 313 A CYS 313 1_555 A SG CYS 322 A CYS 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf4 B SG CYS 32 B CYS 607 1_555 B SG CYS 45 B CYS 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 B SG CYS 41 B CYS 616 1_555 B SG CYS 168 B CYS 743 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf6 B SG CYS 49 B CYS 624 1_555 B SG CYS 159 B CYS 734 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A ND2 ASN 79 A ASN 79 1_555 H C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 A ND2 ASN 102 A ASN 102 1_555 I C1 NAG . A NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale3 A ND2 ASN 134 A ASN 134 1_555 G C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale4 A ND2 ASN 205 A ASN 205 1_555 F C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale5 A ND2 ASN 220 A ASN 220 1_555 J C1 NAG . A NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale6 A ND2 ASN 235 A ASN 235 1_555 E C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale7 A ND2 ASN 247 A ASN 247 1_555 D C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale8 A ND2 ASN 321 A ASN 321 1_555 K C1 NAG . A NAG 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale9 A ND2 ASN 417 A ASN 417 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale10 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale11 C O4 NAG . C NAG 2 1_555 C C1 MAN . C MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? # _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 # 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 O1 GOL sing 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 5LGD _atom_sites.fract_transf_matrix[1][1] 0.007703 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003567 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024554 _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] 0.007938 _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 D 4 NAG A 1 504 460 NAG NAG . E 4 NAG A 1 505 461 NAG NAG . F 4 NAG A 1 506 462 NAG NAG . G 4 NAG A 1 507 463 NAG NAG . H 4 NAG A 1 508 464 NAG NAG . I 4 NAG A 1 509 465 NAG NAG . J 4 NAG A 1 510 466 NAG NAG . K 4 NAG A 1 511 467 NAG NAG . L 5 PLM A 1 512 469 PLM PLM . M 5 PLM A 1 513 470 PLM PLM . N 6 GOL A 1 514 2 GOL GOL . O 6 GOL A 1 515 3 GOL GOL . P 6 GOL A 1 516 4 GOL GOL . Q 6 GOL A 1 517 5 GOL GOL . R 7 TRS A 1 518 1 TRS TRS . S 6 GOL B 1 801 1 GOL GOL . T 7 TRS B 1 802 2 TRS TRS . U 8 HOH A 1 601 50 HOH HOH . U 8 HOH A 2 602 45 HOH HOH . U 8 HOH A 3 603 102 HOH HOH . U 8 HOH A 4 604 19 HOH HOH . U 8 HOH A 5 605 49 HOH HOH . U 8 HOH A 6 606 95 HOH HOH . U 8 HOH A 7 607 24 HOH HOH . U 8 HOH A 8 608 7 HOH HOH . U 8 HOH A 9 609 104 HOH HOH . U 8 HOH A 10 610 41 HOH HOH . U 8 HOH A 11 611 146 HOH HOH . U 8 HOH A 12 612 103 HOH HOH . U 8 HOH A 13 613 105 HOH HOH . U 8 HOH A 14 614 75 HOH HOH . U 8 HOH A 15 615 25 HOH HOH . U 8 HOH A 16 616 64 HOH HOH . U 8 HOH A 17 617 52 HOH HOH . U 8 HOH A 18 618 116 HOH HOH . U 8 HOH A 19 619 83 HOH HOH . U 8 HOH A 20 620 17 HOH HOH . U 8 HOH A 21 621 86 HOH HOH . U 8 HOH A 22 622 117 HOH HOH . U 8 HOH A 23 623 99 HOH HOH . U 8 HOH A 24 624 47 HOH HOH . U 8 HOH A 25 625 92 HOH HOH . U 8 HOH A 26 626 88 HOH HOH . U 8 HOH A 27 627 59 HOH HOH . U 8 HOH A 28 628 46 HOH HOH . U 8 HOH A 29 629 90 HOH HOH . U 8 HOH A 30 630 4 HOH HOH . U 8 HOH A 31 631 16 HOH HOH . U 8 HOH A 32 632 21 HOH HOH . U 8 HOH A 33 633 98 HOH HOH . U 8 HOH A 34 634 72 HOH HOH . U 8 HOH A 35 635 76 HOH HOH . U 8 HOH A 36 636 14 HOH HOH . U 8 HOH A 37 637 2 HOH HOH . U 8 HOH A 38 638 39 HOH HOH . U 8 HOH A 39 639 42 HOH HOH . U 8 HOH A 40 640 23 HOH HOH . U 8 HOH A 41 641 68 HOH HOH . U 8 HOH A 42 642 26 HOH HOH . U 8 HOH A 43 643 43 HOH HOH . U 8 HOH A 44 644 107 HOH HOH . U 8 HOH A 45 645 3 HOH HOH . U 8 HOH A 46 646 18 HOH HOH . U 8 HOH A 47 647 15 HOH HOH . U 8 HOH A 48 648 5 HOH HOH . U 8 HOH A 49 649 65 HOH HOH . U 8 HOH A 50 650 38 HOH HOH . U 8 HOH A 51 651 22 HOH HOH . U 8 HOH A 52 652 71 HOH HOH . U 8 HOH A 53 653 78 HOH HOH . U 8 HOH A 54 654 150 HOH HOH . U 8 HOH A 55 655 1 HOH HOH . U 8 HOH A 56 656 40 HOH HOH . U 8 HOH A 57 657 145 HOH HOH . U 8 HOH A 58 658 61 HOH HOH . U 8 HOH A 59 659 10 HOH HOH . U 8 HOH A 60 660 12 HOH HOH . U 8 HOH A 61 661 35 HOH HOH . U 8 HOH A 62 662 110 HOH HOH . U 8 HOH A 63 663 96 HOH HOH . U 8 HOH A 64 664 115 HOH HOH . U 8 HOH A 65 665 100 HOH HOH . U 8 HOH A 66 666 140 HOH HOH . U 8 HOH A 67 667 60 HOH HOH . U 8 HOH A 68 668 53 HOH HOH . U 8 HOH A 69 669 114 HOH HOH . U 8 HOH A 70 670 34 HOH HOH . U 8 HOH A 71 671 84 HOH HOH . U 8 HOH A 72 672 113 HOH HOH . U 8 HOH A 73 673 48 HOH HOH . U 8 HOH A 74 674 77 HOH HOH . U 8 HOH A 75 675 111 HOH HOH . U 8 HOH A 76 676 74 HOH HOH . U 8 HOH A 77 677 81 HOH HOH . U 8 HOH A 78 678 133 HOH HOH . U 8 HOH A 79 679 127 HOH HOH . U 8 HOH A 80 680 128 HOH HOH . U 8 HOH A 81 681 109 HOH HOH . U 8 HOH A 82 682 31 HOH HOH . U 8 HOH A 83 683 132 HOH HOH . U 8 HOH A 84 684 91 HOH HOH . U 8 HOH A 85 685 11 HOH HOH . U 8 HOH A 86 686 149 HOH HOH . U 8 HOH A 87 687 93 HOH HOH . U 8 HOH A 88 688 37 HOH HOH . U 8 HOH A 89 689 73 HOH HOH . U 8 HOH A 90 690 131 HOH HOH . U 8 HOH A 91 691 13 HOH HOH . U 8 HOH A 92 692 80 HOH HOH . U 8 HOH A 93 693 79 HOH HOH . U 8 HOH A 94 694 148 HOH HOH . U 8 HOH A 95 695 55 HOH HOH . U 8 HOH A 96 696 57 HOH HOH . U 8 HOH A 97 697 106 HOH HOH . U 8 HOH A 98 698 51 HOH HOH . U 8 HOH A 99 699 32 HOH HOH . U 8 HOH A 100 700 141 HOH HOH . U 8 HOH A 101 701 29 HOH HOH . U 8 HOH A 102 702 9 HOH HOH . U 8 HOH A 103 703 112 HOH HOH . U 8 HOH A 104 704 30 HOH HOH . U 8 HOH A 105 705 87 HOH HOH . U 8 HOH A 106 706 67 HOH HOH . U 8 HOH A 107 707 69 HOH HOH . U 8 HOH A 108 708 44 HOH HOH . U 8 HOH A 109 709 89 HOH HOH . U 8 HOH A 110 710 147 HOH HOH . U 8 HOH A 111 711 130 HOH HOH . U 8 HOH A 112 712 94 HOH HOH . U 8 HOH A 113 713 70 HOH HOH . U 8 HOH A 114 714 134 HOH HOH . U 8 HOH A 115 715 97 HOH HOH . U 8 HOH A 116 716 66 HOH HOH . U 8 HOH A 117 717 101 HOH HOH . U 8 HOH A 118 718 108 HOH HOH . U 8 HOH A 119 719 36 HOH HOH . V 8 HOH B 1 901 119 HOH HOH . V 8 HOH B 2 902 142 HOH HOH . V 8 HOH B 3 903 139 HOH HOH . V 8 HOH B 4 904 137 HOH HOH . V 8 HOH B 5 905 136 HOH HOH . V 8 HOH B 6 906 129 HOH HOH . V 8 HOH B 7 907 122 HOH HOH . V 8 HOH B 8 908 8 HOH HOH . V 8 HOH B 9 909 28 HOH HOH . V 8 HOH B 10 910 27 HOH HOH . V 8 HOH B 11 911 62 HOH HOH . V 8 HOH B 12 912 6 HOH HOH . V 8 HOH B 13 913 33 HOH HOH . V 8 HOH B 14 914 82 HOH HOH . V 8 HOH B 15 915 120 HOH HOH . V 8 HOH B 16 916 135 HOH HOH . V 8 HOH B 17 917 143 HOH HOH . V 8 HOH B 18 918 138 HOH HOH . V 8 HOH B 19 919 123 HOH HOH . V 8 HOH B 20 920 151 HOH HOH . V 8 HOH B 21 921 85 HOH HOH . V 8 HOH B 22 922 124 HOH HOH . V 8 HOH B 23 923 144 HOH HOH . V 8 HOH B 24 924 20 HOH HOH . V 8 HOH B 25 925 54 HOH HOH . V 8 HOH B 26 926 121 HOH HOH . V 8 HOH B 27 927 118 HOH HOH . V 8 HOH B 28 928 152 HOH HOH . V 8 HOH B 29 929 56 HOH HOH . V 8 HOH B 30 930 125 HOH HOH . V 8 HOH B 31 931 126 HOH HOH . V 8 HOH B 32 932 63 HOH HOH . V 8 HOH B 33 933 58 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 . . . P 6 -28.493 -21.406 14.748 1 60.89 ? C1 GOL 516 A 1 HETATM 2 O O1 GOL . . . P 6 -28.226 -22.385 13.757 1 60.31 ? O1 GOL 516 A 1 HETATM 3 C C2 GOL . . . P 6 -27.709 -20.136 14.505 1 64.13 ? C2 GOL 516 A 1 HETATM 4 O O2 GOL . . . P 6 -28.215 -19.452 13.352 1 66.39 ? O2 GOL 516 A 1 HETATM 5 C C3 GOL . . . P 6 -27.798 -19.23 15.711 1 64.1 ? C3 GOL 516 A 1 HETATM 6 O O3 GOL . . . P 6 -27.188 -19.836 16.847 1 66.02 ? O3 GOL 516 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 42 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 6 #