data_7JPI # _model_server_result.job_id '_Ras1Bykq4GcWGgLAQtEYQ' _model_server_result.datetime_utc '2024-11-24 17:32:46' _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 7jpi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 7JPI # _exptl.entry_id 7JPI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 120 _cell.entry_id 7JPI _cell.length_a 114.583 _cell.length_b 114.583 _cell.length_c 312.379 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7JPI _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall 'R 3 2"' _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,G,H,I,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 F N N ? 5 G N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 4 4 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 4 5 4 MAN MAN C1 O1 . O3 HO3 . sing 6 ? 4 6 3 MAN BMA C1 O1 . O3 HO3 . 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 F 1 NAG A 479 NAG 3 n C NAG 2 F 2 NAG A 480 NAG 3 n D NAG 1 H 1 NAG A 485 NAG 3 n D NAG 2 H 2 NAG A 488 NAG 4 n E NAG 1 C 1 NAG B 630 NAG 4 n E NAG 2 C 2 NAG B 631 NAG 4 n E BMA 3 C 3 BMA B 632 BMA 4 n E MAN 4 C 4 MAN B 633 MAN 4 n E MAN 5 C 5 MAN B 635 MAN 4 n E MAN 6 C 6 MAN B 636 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 53 A CYS 53 1_555 B SG CYS 108 B CYS 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 108 A CYS 108 1_555 A SG CYS 135 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 121 A CYS 121 1_555 A SG CYS 147 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 B SG CYS 10 B CYS 511 1_555 B SG CYS 55 B CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 B SG CYS 100 B CYS 601 1_555 B SG CYS 107 B CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 238 A ASN 238 1_555 C C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 A ND2 ASN 257 A ASN 257 1_555 D C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 268 A ASN 268 1_555 H C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 B ND2 ASN 62 B ASN 563 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 C O4 NAG . F NAG 1 1_555 C C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale6 D O4 NAG . H NAG 1 1_555 D C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale7 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? covale ? covale8 E O4 NAG . C NAG 2 1_555 E C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale9 E O6 BMA . C BMA 3 1_555 E C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale10 E O3 BMA . C BMA 3 1_555 E C1 MAN . C MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale11 E O3 MAN . C MAN 4 1_555 E C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? # _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 153 n n C1 C2 GOL sing 154 n n C1 H11 GOL sing 155 n n C1 H12 GOL sing 156 n n O1 HO1 GOL sing 157 n n C2 O2 GOL sing 158 n n C2 C3 GOL sing 159 n n C2 H2 GOL sing 160 n n O2 HO2 GOL sing 161 n n C3 O3 GOL sing 162 n n C3 H31 GOL sing 163 n n C3 H32 GOL sing 164 n n O3 HO3 GOL sing 165 n n # _atom_sites.entry_id 7JPI _atom_sites.fract_transf_matrix[1][1] 0.008727 _atom_sites.fract_transf_matrix[1][2] 0.005039 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010077 _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] 0.003201 _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 F 5 GOL A 1 501 2 GOL GOL . G 5 GOL A 1 502 3 GOL GOL . H 6 NAG A 1 503 487 NAG NAG . I 7 PO4 A 1 504 1 PO4 PO4 . J 8 HOH A 1 601 73 HOH HOH . J 8 HOH A 2 602 171 HOH HOH . J 8 HOH A 3 603 1 HOH HOH . J 8 HOH A 4 604 44 HOH HOH . J 8 HOH A 5 605 110 HOH HOH . J 8 HOH A 6 606 108 HOH HOH . J 8 HOH A 7 607 161 HOH HOH . J 8 HOH A 8 608 151 HOH HOH . J 8 HOH A 9 609 71 HOH HOH . J 8 HOH A 10 610 140 HOH HOH . J 8 HOH A 11 611 19 HOH HOH . J 8 HOH A 12 612 58 HOH HOH . J 8 HOH A 13 613 100 HOH HOH . J 8 HOH A 14 614 57 HOH HOH . J 8 HOH A 15 615 43 HOH HOH . J 8 HOH A 16 616 76 HOH HOH . J 8 HOH A 17 617 152 HOH HOH . J 8 HOH A 18 618 79 HOH HOH . J 8 HOH A 19 619 158 HOH HOH . J 8 HOH A 20 620 9 HOH HOH . J 8 HOH A 21 621 25 HOH HOH . J 8 HOH A 22 622 28 HOH HOH . J 8 HOH A 23 623 54 HOH HOH . J 8 HOH A 24 624 169 HOH HOH . J 8 HOH A 25 625 150 HOH HOH . J 8 HOH A 26 626 141 HOH HOH . J 8 HOH A 27 627 120 HOH HOH . J 8 HOH A 28 628 106 HOH HOH . J 8 HOH A 29 629 38 HOH HOH . J 8 HOH A 30 630 6 HOH HOH . J 8 HOH A 31 631 88 HOH HOH . J 8 HOH A 32 632 66 HOH HOH . J 8 HOH A 33 633 40 HOH HOH . J 8 HOH A 34 634 32 HOH HOH . J 8 HOH A 35 635 83 HOH HOH . J 8 HOH A 36 636 56 HOH HOH . J 8 HOH A 37 637 149 HOH HOH . J 8 HOH A 38 638 64 HOH HOH . J 8 HOH A 39 639 116 HOH HOH . J 8 HOH A 40 640 45 HOH HOH . J 8 HOH A 41 641 176 HOH HOH . J 8 HOH A 42 642 81 HOH HOH . J 8 HOH A 43 643 63 HOH HOH . J 8 HOH A 44 644 4 HOH HOH . J 8 HOH A 45 645 16 HOH HOH . J 8 HOH A 46 646 48 HOH HOH . J 8 HOH A 47 647 159 HOH HOH . J 8 HOH A 48 648 86 HOH HOH . J 8 HOH A 49 649 78 HOH HOH . J 8 HOH A 50 650 97 HOH HOH . J 8 HOH A 51 651 29 HOH HOH . J 8 HOH A 52 652 131 HOH HOH . J 8 HOH A 53 653 49 HOH HOH . J 8 HOH A 54 654 139 HOH HOH . J 8 HOH A 55 655 172 HOH HOH . J 8 HOH A 56 656 98 HOH HOH . J 8 HOH A 57 657 130 HOH HOH . J 8 HOH A 58 658 165 HOH HOH . J 8 HOH A 59 659 80 HOH HOH . J 8 HOH A 60 660 5 HOH HOH . J 8 HOH A 61 661 101 HOH HOH . J 8 HOH A 62 662 67 HOH HOH . J 8 HOH A 63 663 115 HOH HOH . J 8 HOH A 64 664 123 HOH HOH . J 8 HOH A 65 665 92 HOH HOH . J 8 HOH A 66 666 55 HOH HOH . J 8 HOH A 67 667 15 HOH HOH . J 8 HOH A 68 668 23 HOH HOH . J 8 HOH A 69 669 129 HOH HOH . J 8 HOH A 70 670 61 HOH HOH . J 8 HOH A 71 671 107 HOH HOH . J 8 HOH A 72 672 99 HOH HOH . J 8 HOH A 73 673 31 HOH HOH . J 8 HOH A 74 674 8 HOH HOH . J 8 HOH A 75 675 77 HOH HOH . J 8 HOH A 76 676 7 HOH HOH . J 8 HOH A 77 677 117 HOH HOH . J 8 HOH A 78 678 84 HOH HOH . J 8 HOH A 79 679 178 HOH HOH . J 8 HOH A 80 680 41 HOH HOH . J 8 HOH A 81 681 109 HOH HOH . J 8 HOH A 82 682 72 HOH HOH . J 8 HOH A 83 683 59 HOH HOH . J 8 HOH A 84 684 162 HOH HOH . J 8 HOH A 85 685 175 HOH HOH . J 8 HOH A 86 686 177 HOH HOH . J 8 HOH A 87 687 121 HOH HOH . J 8 HOH A 88 688 27 HOH HOH . J 8 HOH A 89 689 160 HOH HOH . J 8 HOH A 90 692 168 HOH HOH . K 8 HOH B 1 701 156 HOH HOH . K 8 HOH B 2 702 93 HOH HOH . K 8 HOH B 3 703 75 HOH HOH . K 8 HOH B 4 704 125 HOH HOH . K 8 HOH B 5 705 94 HOH HOH . K 8 HOH B 6 706 155 HOH HOH . K 8 HOH B 7 707 30 HOH HOH . K 8 HOH B 8 708 154 HOH HOH . K 8 HOH B 9 709 36 HOH HOH . K 8 HOH B 10 710 11 HOH HOH . K 8 HOH B 11 711 39 HOH HOH . K 8 HOH B 12 712 147 HOH HOH . K 8 HOH B 13 713 74 HOH HOH . K 8 HOH B 14 714 153 HOH HOH . K 8 HOH B 15 715 35 HOH HOH . K 8 HOH B 16 716 104 HOH HOH . K 8 HOH B 17 717 144 HOH HOH . K 8 HOH B 18 718 142 HOH HOH . K 8 HOH B 19 719 143 HOH HOH . K 8 HOH B 20 720 105 HOH HOH . K 8 HOH B 21 721 157 HOH HOH . K 8 HOH B 22 722 42 HOH HOH . K 8 HOH B 23 723 163 HOH HOH . K 8 HOH B 24 724 133 HOH HOH . K 8 HOH B 25 725 82 HOH HOH . K 8 HOH B 26 726 69 HOH HOH . K 8 HOH B 27 727 164 HOH HOH . K 8 HOH B 28 728 132 HOH HOH . K 8 HOH B 29 729 91 HOH HOH . K 8 HOH B 30 730 47 HOH HOH . K 8 HOH B 31 731 33 HOH HOH . K 8 HOH B 32 732 21 HOH HOH . K 8 HOH B 33 733 17 HOH HOH . K 8 HOH B 34 734 2 HOH HOH . K 8 HOH B 35 735 60 HOH HOH . K 8 HOH B 36 736 22 HOH HOH . K 8 HOH B 37 737 50 HOH HOH . K 8 HOH B 38 738 14 HOH HOH . K 8 HOH B 39 739 46 HOH HOH . K 8 HOH B 40 740 18 HOH HOH . K 8 HOH B 41 741 145 HOH HOH . K 8 HOH B 42 742 170 HOH HOH . K 8 HOH B 43 743 37 HOH HOH . K 8 HOH B 44 744 20 HOH HOH . K 8 HOH B 45 745 136 HOH HOH . K 8 HOH B 46 746 52 HOH HOH . K 8 HOH B 47 747 111 HOH HOH . K 8 HOH B 48 748 62 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 . . . F 5 -7.346 -12.872 -14.431 1 72.47 ? C1 GOL 501 A 1 HETATM 2 O O1 GOL . . . F 5 -6.784 -12.961 -15.7 1 70.88 ? O1 GOL 501 A 1 HETATM 3 C C2 GOL . . . F 5 -7.245 -11.398 -14.003 1 88.46 ? C2 GOL 501 A 1 HETATM 4 O O2 GOL . . . F 5 -8.05 -10.578 -14.778 1 64.47 ? O2 GOL 501 A 1 HETATM 5 C C3 GOL . . . F 5 -7.668 -11.397 -12.524 1 92.15 ? C3 GOL 501 A 1 HETATM 6 O O3 GOL . . . F 5 -7.752 -10.065 -12.131 1 78.7 ? O3 GOL 501 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 6 #