data_8SRK # _model_server_result.job_id mbX998xa0oB-gB1qJeJCAw _model_server_result.datetime_utc '2024-12-26 20:32:30' _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 8srk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":1701}' # _entry.id 8SRK # _exptl.entry_id 8SRK _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 559.316 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE-5-DIPHOSPHORIBOSE _entity.pdbx_number_of_molecules 4 _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 8SRK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SRK _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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,W,X,Y,Z,AA,BA _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 ? _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 ? 2 E N N ? 2 K N N ? 2 Q N N ? 2 Y 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 disulf ? disulf1 A SG CYS 997 A CYS 997 1_555 A SG CYS 1006 A CYS 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 B SG CYS 997 B CYS 997 1_555 B SG CYS 1006 B CYS 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 C SG CYS 997 C CYS 997 1_555 C SG CYS 1006 C CYS 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 D SG CYS 997 D CYS 997 1_555 D SG CYS 1006 D CYS 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc1 A O LEU 621 A LEU 621 1_555 G CA CA . A CA 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc2 A O GLY 623 A GLY 623 1_555 G CA CA . A CA 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc3 A OD1 ASN 869 A ASN 869 1_555 F CA CA . A CA 1702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? metalc ? metalc4 B O LEU 621 B LEU 621 1_555 M CA CA . B CA 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc5 B O GLY 623 B GLY 623 1_555 M CA CA . B CA 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc6 B OD1 ASN 869 B ASN 869 1_555 L CA CA . B CA 1702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? metalc ? metalc7 C O LEU 621 C LEU 621 1_555 S CA CA . C CA 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc8 C O GLY 623 C GLY 623 1_555 S CA CA . C CA 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc9 C OD1 ASN 869 C ASN 869 1_555 R CA CA . C CA 1702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc10 D O LEU 621 D LEU 621 1_555 AA CA CA . D CA 6005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc11 D O GLY 623 D GLY 623 1_555 AA CA CA . D CA 6005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc12 D OD1 ASN 869 D ASN 869 1_555 Z CA CA . D CA 6004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id APR _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE-5-DIPHOSPHORIBOSE _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 N1 C2 APR sing 13 n y N1 C6 APR doub 14 n y C2 N3 APR doub 15 n y C2 H2 APR sing 16 n n N3 C4 APR sing 17 n y C4 C5 APR doub 18 n y C4 N9 APR sing 19 n y C5 C6 APR sing 20 n y C5 N7 APR sing 21 n y C6 N6 APR sing 22 n n N6 H61 APR sing 23 n n N6 H62 APR sing 24 n n N7 C8 APR doub 25 n y C8 N9 APR sing 26 n y C8 H8 APR sing 27 n n N9 C1' APR sing 28 n n C1' C2' APR sing 29 n n C1' O4' APR sing 30 n n C1' "H'1" APR sing 31 n n C2' O2' APR sing 32 n n C2' C3' APR sing 33 n n C2' "H'2" APR sing 34 n n O2' "HO'2" APR sing 35 n n C3' O3' APR sing 36 n n C3' C4' APR sing 37 n n C3' "H'3" APR sing 38 n n O3' "HO'3" APR sing 39 n n O4' C4' APR sing 40 n n C4' C5' APR sing 41 n n C4' "H'4" APR sing 42 n n C5' O5' APR sing 43 n n C5' "H5'1" APR sing 44 n n C5' "H5'2" APR sing 45 n n O5' PA APR sing 46 n n PA O1A APR doub 47 n n PA O2A APR sing 48 n n PA O3A APR sing 49 n n O2A HOA2 APR sing 50 n n O3A PB APR sing 51 n n PB O1B APR doub 52 n n PB O2B APR sing 53 n n PB O5D APR sing 54 n n O2B HOB2 APR sing 55 n n O5D C5D APR sing 56 n n C5D C4D APR sing 57 n n C5D H5R1 APR sing 58 n n C5D H5R2 APR sing 59 n n O4D C1D APR sing 60 n n O4D C4D APR sing 61 n n O1D C1D APR sing 62 n n O1D HOR1 APR sing 63 n n C1D C2D APR sing 64 n n C1D "HR'1" APR sing 65 n n O2D C2D APR sing 66 n n O2D HOR2 APR sing 67 n n C2D C3D APR sing 68 n n C2D "HR'2" APR sing 69 n n O3D C3D APR sing 70 n n O3D HOR3 APR sing 71 n n C3D C4D APR sing 72 n n C3D "HR'3" APR sing 73 n n C4D "HR'4" APR sing 74 n n # _atom_sites.entry_id 8SRK _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 2 APR A 1 1701 1701 APR APR . F 3 CA A 1 1702 3001 CA CA . G 3 CA A 1 1703 3002 CA CA . H 4 CLR A 1 1704 6003 CLR CLR . I 4 CLR A 1 1705 6001 CLR CLR . J 4 CLR A 1 1706 6002 CLR CLR . K 2 APR B 1 1701 1701 APR APR . L 3 CA B 1 1702 3001 CA CA . M 3 CA B 1 1703 3002 CA CA . N 4 CLR B 1 1704 6003 CLR CLR . O 4 CLR B 1 1705 6001 CLR CLR . P 4 CLR B 1 1706 6002 CLR CLR . Q 2 APR C 1 1701 1701 APR APR . R 3 CA C 1 1702 3001 CA CA . S 3 CA C 1 1703 3002 CA CA . T 4 CLR C 1 1704 6003 CLR CLR . U 4 CLR C 1 1705 6001 CLR CLR . V 4 CLR C 1 1706 6002 CLR CLR . W 4 CLR D 1 6001 6001 CLR CLR . X 4 CLR D 1 6002 6002 CLR CLR . Y 2 APR D 1 6003 1701 APR APR . Z 3 CA D 1 6004 3001 CA CA . AA 3 CA D 1 6005 3002 CA CA . BA 4 CLR D 1 6006 6003 CLR CLR . # 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 N N1 APR . . . Q 2 170.283 128.318 118.878 1 176.73 ? N1 APR 1701 C 1 HETATM 2 C C2 APR . . . Q 2 171.538 128.13 118.433 1 178 ? C2 APR 1701 C 1 HETATM 3 N N3 APR . . . Q 2 171.857 128.028 117.136 1 177.29 ? N3 APR 1701 C 1 HETATM 4 C C4 APR . . . Q 2 170.902 128.116 116.186 1 178.89 ? C4 APR 1701 C 1 HETATM 5 C C5 APR . . . Q 2 169.506 128.321 116.588 1 178.83 ? C5 APR 1701 C 1 HETATM 6 C C6 APR . . . Q 2 169.234 128.423 118.038 1 176.92 ? C6 APR 1701 C 1 HETATM 7 N N6 APR . . . Q 2 167.979 128.612 118.507 1 176.08 ? N6 APR 1701 C 1 HETATM 8 N N7 APR . . . Q 2 168.782 128.367 115.457 1 180.46 ? N7 APR 1701 C 1 HETATM 9 C C8 APR . . . Q 2 169.638 128.208 114.418 1 181.44 ? C8 APR 1701 C 1 HETATM 10 N N9 APR . . . Q 2 170.898 128.056 114.86 1 181.96 ? N9 APR 1701 C 1 HETATM 11 C C1' APR . . . Q 2 172.092 127.855 114.018 1 181.61 ? C1' APR 1701 C 1 HETATM 12 C C2' APR . . . Q 2 171.697 128.105 112.579 1 181.99 ? C2' APR 1701 C 1 HETATM 13 O O2' APR . . . Q 2 171.969 126.937 111.805 1 180.66 ? O2' APR 1701 C 1 HETATM 14 C C3' APR . . . Q 2 172.554 129.259 112.11 1 180.8 ? C3' APR 1701 C 1 HETATM 15 O O3' APR . . . Q 2 173.307 128.865 110.962 1 178.69 ? O3' APR 1701 C 1 HETATM 16 O O4' APR . . . Q 2 173.094 128.805 114.38 1 177.92 ? O4' APR 1701 C 1 HETATM 17 C C4' APR . . . Q 2 173.488 129.595 113.26 1 179.57 ? C4' APR 1701 C 1 HETATM 18 C C5' APR . . . Q 2 173.402 131.068 113.622 1 180.64 ? C5' APR 1701 C 1 HETATM 19 O O5' APR . . . Q 2 172.049 131.488 113.489 1 185.18 ? O5' APR 1701 C 1 HETATM 20 P PA APR . . . Q 2 171.711 132.992 113.036 1 186.75 ? PA APR 1701 C 1 HETATM 21 O O1A APR . . . Q 2 172.626 133.925 113.786 1 180.49 ? O1A APR 1701 C 1 HETATM 22 O O2A APR . . . Q 2 171.687 133.048 111.529 1 177.54 ? O2A APR 1701 C 1 HETATM 23 O O3A APR . . . Q 2 170.224 133.2 113.614 1 182.89 ? O3A APR 1701 C 1 HETATM 24 P PB APR . . . Q 2 168.946 132.415 113.032 1 184.2 ? PB APR 1701 C 1 HETATM 25 O O1B APR . . . Q 2 169.349 131.44 111.954 1 178.02 ? O1B APR 1701 C 1 HETATM 26 O O2B APR . . . Q 2 167.875 133.439 112.767 1 180.92 ? O2B APR 1701 C 1 HETATM 27 O O5D APR . . . Q 2 168.451 131.564 114.295 1 181.26 ? O5D APR 1701 C 1 HETATM 28 C C5D APR . . . Q 2 167.053 131.509 114.546 1 180.17 ? C5D APR 1701 C 1 HETATM 29 O O4D APR . . . Q 2 168.039 131.478 116.751 1 182.1 ? O4D APR 1701 C 1 HETATM 30 O O1D APR . . . Q 2 168.646 133.297 118.089 1 179.01 ? O1D APR 1701 C 1 HETATM 31 C C1D APR . . . Q 2 167.787 132.16 117.982 1 179.78 ? C1D APR 1701 C 1 HETATM 32 O O2D APR . . . Q 2 165.585 131.982 118.981 1 177.3 ? O2D APR 1701 C 1 HETATM 33 C C2D APR . . . Q 2 166.342 132.626 117.953 1 178.54 ? C2D APR 1701 C 1 HETATM 34 O O3D APR . . . Q 2 164.525 131.618 116.71 1 179.36 ? O3D APR 1701 C 1 HETATM 35 C C3D APR . . . Q 2 165.802 132.248 116.59 1 179.56 ? C3D APR 1701 C 1 HETATM 36 C C4D APR . . . Q 2 166.823 131.278 116.028 1 180.93 ? C4D APR 1701 C 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 81 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 36 #