data_7SCD # _model_server_result.job_id WTdiFLhYb9IBIX0RHvvxfA _model_server_result.datetime_utc '2024-10-19 21:23:56' _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 7scd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1401}' # _entry.id 7SCD # _exptl.entry_id 7SCD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 7SCD _cell.length_a 55.84 _cell.length_b 58.82 _cell.length_c 153.11 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7SCD _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' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 SGN BDP C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BDP SGN C1 O1 . O4 HO4 . sing 3 ? 2 4 3 SGN BDP C1 O1 . O4 HO4 . sing 4 ? 2 5 4 BDP SGN C1 O1 . O4 HO4 . sing 5 ? 2 6 5 SGN BDP 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 2 n B BDP 1 C 1 BDP C 6 BDP 2 n B SGN 2 C 2 SGN C 5 SGN 2 n B BDP 3 C 3 BDP C 4 BDP 2 n B SGN 4 C 4 SGN C 3 SGN 2 n B BDP 5 C 5 BDP C 2 BDP 2 n B SGN 6 C 6 SGN C 1 SGN # 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 33 A CYS 33 1_555 A SG CYS 36 A CYS 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf2 A SG CYS 320 A CYS 1294 1_555 A SG CYS 330 A CYS 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? covale ? covale1 B O4 BDP . C BDP 1 1_555 B C1 SGN . C SGN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 B O4 SGN . C SGN 2 1_555 B C1 BDP . C BDP 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 B O4 BDP . C BDP 3 1_555 B C1 SGN . C SGN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale4 B O4 SGN . C SGN 4 1_555 B C1 BDP . C BDP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale5 B O4 BDP . C BDP 5 1_555 B C1 SGN . C SGN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 7SCD _atom_sites.fract_transf_matrix[1][1] 0.017908 _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] 0.017001 _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] 0.006531 _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 3 A3P A 1 1401 600 A3P A3P . D 4 HOH A 1 1501 11 HOH HOH . D 4 HOH A 2 1502 5 HOH HOH . D 4 HOH A 3 1503 2 HOH HOH . D 4 HOH A 4 1504 10 HOH HOH . D 4 HOH A 5 1505 6 HOH HOH . D 4 HOH A 6 1506 8 HOH HOH . D 4 HOH A 7 1507 9 HOH HOH . D 4 HOH A 8 1508 7 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 P P1 A3P . . . C 3 -16.592 24.33 -22.976 0.7 35.68 ? P1 A3P 1401 A 1 HETATM 2 O O1P A3P . . . C 3 -16.716 25.733 -23.523 0.7 33.71 ? O1P A3P 1401 A 1 HETATM 3 O O2P A3P . . . C 3 -15.609 24.288 -21.828 0.7 18.43 ? O2P A3P 1401 A 1 HETATM 4 O O3P A3P . . . C 3 -17.902 23.626 -22.705 0.7 43.9 ? O3P A3P 1401 A 1 HETATM 5 P P2 A3P . . . C 3 -15.016 18.599 -26.908 0.7 18.29 ? P2 A3P 1401 A 1 HETATM 6 O O4P A3P . . . C 3 -16.14 18.442 -27.902 0.7 24.04 ? O4P A3P 1401 A 1 HETATM 7 O O5P A3P . . . C 3 -13.721 17.977 -27.381 0.7 20.32 ? O5P A3P 1401 A 1 HETATM 8 O O6P A3P . . . C 3 -15.415 18.123 -25.532 0.7 19.87 ? O6P A3P 1401 A 1 HETATM 9 O O5' A3P . . . C 3 -14.763 20.206 -26.801 0.7 28.5 ? O5' A3P 1401 A 1 HETATM 10 C C5' A3P . . . C 3 -15.679 21.058 -26.125 0.7 38.91 ? C5' A3P 1401 A 1 HETATM 11 C C4' A3P . . . C 3 -15.276 22.511 -26.226 0.7 32.48 ? C4' A3P 1401 A 1 HETATM 12 O O4' A3P . . . C 3 -15.177 22.971 -27.61 0.7 34.01 ? O4' A3P 1401 A 1 HETATM 13 C C3' A3P . . . C 3 -16.228 23.483 -25.559 0.7 35.59 ? C3' A3P 1401 A 1 HETATM 14 O O3' A3P . . . C 3 -15.898 23.466 -24.173 0.7 28.51 ? O3' A3P 1401 A 1 HETATM 15 C C2' A3P . . . C 3 -15.961 24.811 -26.292 0.7 31.34 ? C2' A3P 1401 A 1 HETATM 16 O O2' A3P . . . C 3 -15.003 25.654 -25.651 0.7 43.27 ? O2' A3P 1401 A 1 HETATM 17 C C1' A3P . . . C 3 -15.44 24.372 -27.676 0.7 23.26 ? C1' A3P 1401 A 1 HETATM 18 N N9 A3P . . . C 3 -16.062 24.882 -28.943 0.7 20.56 ? N9 A3P 1401 A 1 HETATM 19 C C8 A3P . . . C 3 -15.362 25.198 -30.068 0.7 29.85 ? C8 A3P 1401 A 1 HETATM 20 N N7 A3P . . . C 3 -16.11 25.641 -31.032 0.7 39.56 ? N7 A3P 1401 A 1 HETATM 21 C C5 A3P . . . C 3 -17.391 25.628 -30.508 0.7 26.97 ? C5 A3P 1401 A 1 HETATM 22 C C6 A3P . . . C 3 -18.603 26.004 -31.114 0.7 24.43 ? C6 A3P 1401 A 1 HETATM 23 N N6 A3P . . . C 3 -18.677 26.472 -32.373 0.7 20.43 ? N6 A3P 1401 A 1 HETATM 24 N N1 A3P . . . C 3 -19.727 25.894 -30.368 0.7 25.32 ? N1 A3P 1401 A 1 HETATM 25 C C2 A3P . . . C 3 -19.621 25.435 -29.103 0.7 29.89 ? C2 A3P 1401 A 1 HETATM 26 N N3 A3P . . . C 3 -18.514 25.046 -28.431 0.7 32.06 ? N3 A3P 1401 A 1 HETATM 27 C C4 A3P . . . C 3 -17.402 25.164 -29.194 0.7 25.18 ? C4 A3P 1401 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #