data_8DCF # _model_server_result.job_id b5hjOjSgOPL2PQp3C-pkfw _model_server_result.datetime_utc '2024-11-15 23:56:25' _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 8dcf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":502}' # _entry.id 8DCF # _exptl.entry_id 8DCF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 7 _entity.src_method syn _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 90 _cell.entry_id 8DCF _cell.length_a 81.105 _cell.length_b 137.828 _cell.length_c 149.755 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DCF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,JA 1 1 B,D,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,KA 2 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 ? 7 U N N ? 7 V N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 FRU _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 2 n C GLC 1 C 1 GLC A 502 SUC 2 n C FRU 2 C 2 FRU A 502 SUC 2 n D GLC 1 D 1 GLC B 502 SUC 2 n D FRU 2 D 2 FRU B 502 SUC # 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 C C1 GLC . C GLC 1 1_555 C O2 FRU . C FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale2 D C1 GLC . D GLC 1 1_555 D O2 FRU . D FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? metalc ? metalc1 A SG CYS 118 A CYS 98 1_555 R CU CU . A CU 614 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc2 A NE2 HIS 223 A HIS 203 1_555 R CU CU . A CU 614 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc3 A NE2 HIS 254 A HIS 234 1_555 Q CU CU . A CU 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc4 A NE2 HIS 321 A HIS 301 1_555 P CU CU . A CU 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc5 A OE2 GLU 325 A GLU 305 1_555 P CU CU . A CU 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc6 A NE2 HIS 349 A HIS 329 1_555 Q CU CU . A CU 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc7 E O3G GTP . A GTP 601 1_555 R CU CU . A CU 614 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc8 P CU CU . A CU 612 1_555 JA O HOH . A HOH 735 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc9 P CU CU . A CU 612 1_555 JA O HOH . A HOH 754 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc10 B SG CYS 118 B CYS 98 1_555 FA CU CU . B CU 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc11 B SG CYS 118 B CYS 98 1_555 GA CU CU . B CU 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc12 B NE2 HIS 223 B HIS 203 1_555 GA CU CU . B CU 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc13 B NE2 HIS 254 B HIS 234 1_555 FA CU CU . B CU 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc14 B NE2 HIS 321 B HIS 301 1_555 HA CU CU . B CU 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc15 B OE2 GLU 325 B GLU 305 1_555 HA CU CU . B CU 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc16 B NE2 HIS 349 B HIS 329 1_555 FA CU CU . B CU 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc17 T O3B GTP . B GTP 501 1_555 GA CU CU . B CU 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc18 HA CU CU . B CU 515 1_555 KA O HOH . B HOH 629 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc19 HA CU CU . B CU 515 1_555 KA O HOH . B HOH 643 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc20 HA CU CU . B CU 515 1_555 KA O HOH . B HOH 646 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? # _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 177 n n C1 C2 GOL sing 178 n n C1 H11 GOL sing 179 n n C1 H12 GOL sing 180 n n O1 HO1 GOL sing 181 n n C2 O2 GOL sing 182 n n C2 C3 GOL sing 183 n n C2 H2 GOL sing 184 n n O2 HO2 GOL sing 185 n n C3 O3 GOL sing 186 n n C3 H31 GOL sing 187 n n C3 H32 GOL sing 188 n n O3 HO3 GOL sing 189 n n # _atom_sites.entry_id 8DCF _atom_sites.fract_transf_matrix[1][1] 0.01233 _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] 0.007255 _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] 0.006678 _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 E 3 GTP A 1 601 601 GTP GTP . F 4 SO4 A 1 602 2 SO4 SO4 . G 4 SO4 A 1 603 3 SO4 SO4 . H 4 SO4 A 1 604 4 SO4 SO4 . I 4 SO4 A 1 605 5 SO4 SO4 . J 4 SO4 A 1 606 6 SO4 SO4 . K 4 SO4 A 1 607 10 SO4 SO4 . L 4 SO4 A 1 608 12 SO4 SO4 . M 4 SO4 A 1 609 14 SO4 SO4 . N 4 SO4 A 1 610 15 SO4 SO4 . O 4 SO4 A 1 611 22 SO4 SO4 . P 5 CU A 1 612 5 CU CU . Q 5 CU A 1 613 7 CU CU . R 5 CU A 1 614 8 CU CU . S 6 CL A 1 615 1 CL CL . T 3 GTP B 1 501 501 GTP GTP . U 7 GOL B 1 502 503 GOL GOL . V 7 GOL B 1 503 504 GOL GOL . W 4 SO4 B 1 504 1 SO4 SO4 . X 4 SO4 B 1 505 7 SO4 SO4 . Y 4 SO4 B 1 506 9 SO4 SO4 . Z 4 SO4 B 1 507 11 SO4 SO4 . AA 4 SO4 B 1 508 16 SO4 SO4 . BA 4 SO4 B 1 509 17 SO4 SO4 . CA 4 SO4 B 1 510 18 SO4 SO4 . DA 4 SO4 B 1 511 23 SO4 SO4 . EA 4 SO4 B 1 512 24 SO4 SO4 . FA 5 CU B 1 513 1 CU CU . GA 5 CU B 1 514 2 CU CU . HA 5 CU B 1 515 6 CU CU . IA 6 CL B 1 516 3 CL CL . JA 8 HOH A 1 701 152 HOH HOH . JA 8 HOH A 2 702 111 HOH HOH . JA 8 HOH A 3 703 115 HOH HOH . JA 8 HOH A 4 704 14 HOH HOH . JA 8 HOH A 5 705 91 HOH HOH . JA 8 HOH A 6 706 124 HOH HOH . JA 8 HOH A 7 707 77 HOH HOH . JA 8 HOH A 8 708 26 HOH HOH . JA 8 HOH A 9 709 78 HOH HOH . JA 8 HOH A 10 710 37 HOH HOH . JA 8 HOH A 11 711 2 HOH HOH . JA 8 HOH A 12 712 18 HOH HOH . JA 8 HOH A 13 713 36 HOH HOH . JA 8 HOH A 14 714 151 HOH HOH . JA 8 HOH A 15 715 153 HOH HOH . JA 8 HOH A 16 716 41 HOH HOH . JA 8 HOH A 17 717 146 HOH HOH . JA 8 HOH A 18 718 16 HOH HOH . JA 8 HOH A 19 719 81 HOH HOH . JA 8 HOH A 20 720 82 HOH HOH . JA 8 HOH A 21 721 90 HOH HOH . JA 8 HOH A 22 722 23 HOH HOH . JA 8 HOH A 23 723 15 HOH HOH . JA 8 HOH A 24 724 39 HOH HOH . JA 8 HOH A 25 725 46 HOH HOH . JA 8 HOH A 26 726 34 HOH HOH . JA 8 HOH A 27 727 40 HOH HOH . JA 8 HOH A 28 728 10 HOH HOH . JA 8 HOH A 29 729 8 HOH HOH . JA 8 HOH A 30 730 61 HOH HOH . JA 8 HOH A 31 731 38 HOH HOH . JA 8 HOH A 32 732 86 HOH HOH . JA 8 HOH A 33 733 11 HOH HOH . JA 8 HOH A 34 734 57 HOH HOH . JA 8 HOH A 35 735 48 HOH HOH . JA 8 HOH A 36 736 60 HOH HOH . JA 8 HOH A 37 737 68 HOH HOH . JA 8 HOH A 38 738 120 HOH HOH . JA 8 HOH A 39 739 112 HOH HOH . JA 8 HOH A 40 740 42 HOH HOH . JA 8 HOH A 41 741 35 HOH HOH . JA 8 HOH A 42 742 47 HOH HOH . JA 8 HOH A 43 743 45 HOH HOH . JA 8 HOH A 44 744 128 HOH HOH . JA 8 HOH A 45 745 137 HOH HOH . JA 8 HOH A 46 746 122 HOH HOH . JA 8 HOH A 47 747 13 HOH HOH . JA 8 HOH A 48 748 88 HOH HOH . JA 8 HOH A 49 749 66 HOH HOH . JA 8 HOH A 50 750 131 HOH HOH . JA 8 HOH A 51 751 94 HOH HOH . JA 8 HOH A 52 752 121 HOH HOH . JA 8 HOH A 53 753 129 HOH HOH . JA 8 HOH A 54 754 32 HOH HOH . JA 8 HOH A 55 755 69 HOH HOH . JA 8 HOH A 56 756 133 HOH HOH . JA 8 HOH A 57 757 123 HOH HOH . JA 8 HOH A 58 758 130 HOH HOH . JA 8 HOH A 59 759 132 HOH HOH . JA 8 HOH A 60 760 67 HOH HOH . JA 8 HOH A 61 761 87 HOH HOH . JA 8 HOH A 62 762 125 HOH HOH . KA 8 HOH B 1 601 70 HOH HOH . KA 8 HOH B 2 602 138 HOH HOH . KA 8 HOH B 3 603 62 HOH HOH . KA 8 HOH B 4 604 64 HOH HOH . KA 8 HOH B 5 605 79 HOH HOH . KA 8 HOH B 6 606 30 HOH HOH . KA 8 HOH B 7 607 53 HOH HOH . KA 8 HOH B 8 608 56 HOH HOH . KA 8 HOH B 9 609 110 HOH HOH . KA 8 HOH B 10 610 140 HOH HOH . KA 8 HOH B 11 611 150 HOH HOH . KA 8 HOH B 12 612 31 HOH HOH . KA 8 HOH B 13 613 65 HOH HOH . KA 8 HOH B 14 614 5 HOH HOH . KA 8 HOH B 15 615 99 HOH HOH . KA 8 HOH B 16 616 29 HOH HOH . KA 8 HOH B 17 617 1 HOH HOH . KA 8 HOH B 18 618 4 HOH HOH . KA 8 HOH B 19 619 144 HOH HOH . KA 8 HOH B 20 620 142 HOH HOH . KA 8 HOH B 21 621 92 HOH HOH . KA 8 HOH B 22 622 76 HOH HOH . KA 8 HOH B 23 623 72 HOH HOH . KA 8 HOH B 24 624 22 HOH HOH . KA 8 HOH B 25 625 20 HOH HOH . KA 8 HOH B 26 626 134 HOH HOH . KA 8 HOH B 27 627 21 HOH HOH . KA 8 HOH B 28 628 136 HOH HOH . KA 8 HOH B 29 629 52 HOH HOH . KA 8 HOH B 30 630 93 HOH HOH . KA 8 HOH B 31 631 89 HOH HOH . KA 8 HOH B 32 632 145 HOH HOH . KA 8 HOH B 33 633 58 HOH HOH . KA 8 HOH B 34 634 6 HOH HOH . KA 8 HOH B 35 635 80 HOH HOH . KA 8 HOH B 36 636 54 HOH HOH . KA 8 HOH B 37 637 147 HOH HOH . KA 8 HOH B 38 638 141 HOH HOH . KA 8 HOH B 39 639 106 HOH HOH . KA 8 HOH B 40 640 100 HOH HOH . KA 8 HOH B 41 641 103 HOH HOH . KA 8 HOH B 42 642 107 HOH HOH . KA 8 HOH B 43 643 117 HOH HOH . KA 8 HOH B 44 644 101 HOH HOH . KA 8 HOH B 45 645 95 HOH HOH . KA 8 HOH B 46 646 116 HOH HOH . KA 8 HOH B 47 647 75 HOH HOH . KA 8 HOH B 48 648 85 HOH HOH . KA 8 HOH B 49 649 135 HOH HOH . KA 8 HOH B 50 650 55 HOH HOH . KA 8 HOH B 51 651 3 HOH HOH . KA 8 HOH B 52 652 126 HOH HOH . KA 8 HOH B 53 653 139 HOH HOH . KA 8 HOH B 54 654 143 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 . . . U 7 20.891 3.754 44.602 1 66.97 ? C1 GOL 502 B 1 HETATM 2 O O1 GOL . . . U 7 20.911 5.119 44.897 1 68.1 ? O1 GOL 502 B 1 HETATM 3 C C2 GOL . . . U 7 21.644 3.686 43.294 1 68.72 ? C2 GOL 502 B 1 HETATM 4 O O2 GOL . . . U 7 22.846 4.381 43.396 1 83.59 ? O2 GOL 502 B 1 HETATM 5 C C3 GOL . . . U 7 21.809 2.172 42.945 1 73.15 ? C3 GOL 502 B 1 HETATM 6 O O3 GOL . . . U 7 22.935 2.074 42.084 1 76.8 ? O3 GOL 502 B 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 6 #