data_7KYB # _model_server_result.job_id sW6jaQTSGqqndB2zv8GYwQ _model_server_result.datetime_utc '2024-12-26 20:16:00' _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 7kyb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1602}' # _entry.id 7KYB # _exptl.entry_id 7KYB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-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 7KYB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KYB _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 ? 3 3 2 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 4 2 1 NAG 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 B 1002 NAG 3 n C NAG 2 C 2 NAG B 1003 NAG 3 n C MAN 3 C 3 MAN B 1004 MAN 4 n D NAG 1 D 1 NAG B 1006 NAG 4 n D NAG 2 D 2 NAG B 1007 NAG 4 n E NAG 1 E 1 NAG B 1008 NAG 4 n E NAG 2 E 2 NAG B 1009 NAG # 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 B SG CYS 110 B CYS 110 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 B SG CYS 216 B CYS 216 1_555 B SG CYS 231 B CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? covale ? covale1 B ND2 ASN 113 B ASN 113 1_555 L C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 B ND2 ASN 240 B ASN 240 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale3 B ND2 ASN 256 B ASN 256 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale4 B ND2 ASN 298 B ASN 298 1_555 K C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale5 B ND2 ASN 332 B ASN 332 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 MAN . C MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A O GLN 797 A GLN 797 1_555 J MG MG . A MG 1605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc2 A OE1 GLU 1151 A GLU 1151 1_555 J MG MG . A MG 1605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.983 ? metalc ? metalc3 G O3B ADP . A ADP 1602 1_555 I MG MG . A MG 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc4 G O2A ADP . A ADP 1602 1_555 I MG MG . A MG 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 7KYB _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 F 5 POV A 1 1601 2010 POV POV . G 6 ADP A 1 1602 2201 ADP ADP . H 7 ALF A 1 1603 2202 ALF ALF . I 8 MG A 1 1604 2203 MG MG . J 8 MG A 1 1605 2204 MG MG . K 9 NAG B 1 1001 1001 NAG NAG . L 9 NAG B 1 1002 1005 NAG NAG . # 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 PB ADP . . . G 6 158.504 150.061 147.972 1 47.22 ? PB ADP 1602 A 1 HETATM 2 O O1B ADP . . . G 6 157.778 149.154 147.01 1 47.22 ? O1B ADP 1602 A 1 HETATM 3 O O2B ADP . . . G 6 158.353 149.619 149.395 1 47.22 ? O2B ADP 1602 A 1 HETATM 4 O O3B ADP . . . G 6 158.282 151.535 147.781 1 47.22 ? O3B ADP 1602 A 1 HETATM 5 P PA ADP . . . G 6 161.004 150.72 146.732 1 47.22 ? PA ADP 1602 A 1 HETATM 6 O O1A ADP . . . G 6 161.77 149.804 145.813 1 47.22 ? O1A ADP 1602 A 1 HETATM 7 O O2A ADP . . . G 6 160.265 151.921 146.218 1 47.22 ? O2A ADP 1602 A 1 HETATM 8 O O3A ADP . . . G 6 160.078 149.867 147.73 1 47.22 ? O3A ADP 1602 A 1 HETATM 9 O O5' ADP . . . G 6 162.074 151.251 147.786 1 47.22 ? O5' ADP 1602 A 1 HETATM 10 C C5' ADP . . . G 6 161.904 150.838 149.128 1 47.22 ? C5' ADP 1602 A 1 HETATM 11 C C4' ADP . . . G 6 163.06 151.346 149.954 1 47.22 ? C4' ADP 1602 A 1 HETATM 12 O O4' ADP . . . G 6 163.479 152.58 149.4 1 47.22 ? O4' ADP 1602 A 1 HETATM 13 C C3' ADP . . . G 6 162.59 151.602 151.364 1 47.22 ? C3' ADP 1602 A 1 HETATM 14 O O3' ADP . . . G 6 163.367 150.849 152.291 1 47.22 ? O3' ADP 1602 A 1 HETATM 15 C C2' ADP . . . G 6 162.818 153.069 151.605 1 47.22 ? C2' ADP 1602 A 1 HETATM 16 O O2' ADP . . . G 6 163.557 153.224 152.812 1 47.22 ? O2' ADP 1602 A 1 HETATM 17 C C1' ADP . . . G 6 163.62 153.555 150.42 1 47.22 ? C1' ADP 1602 A 1 HETATM 18 N N9 ADP . . . G 6 163.062 154.83 149.933 1 47.22 ? N9 ADP 1602 A 1 HETATM 19 C C8 ADP . . . G 6 161.838 154.985 149.413 1 47.22 ? C8 ADP 1602 A 1 HETATM 20 N N7 ADP . . . G 6 161.615 156.272 149.06 1 47.22 ? N7 ADP 1602 A 1 HETATM 21 C C5 ADP . . . G 6 162.724 156.96 149.362 1 47.22 ? C5 ADP 1602 A 1 HETATM 22 C C6 ADP . . . G 6 163.156 158.36 149.248 1 47.22 ? C6 ADP 1602 A 1 HETATM 23 N N6 ADP . . . G 6 162.332 159.29 148.727 1 47.22 ? N6 ADP 1602 A 1 HETATM 24 N N1 ADP . . . G 6 164.387 158.676 149.675 1 47.22 ? N1 ADP 1602 A 1 HETATM 25 C C2 ADP . . . G 6 165.206 157.752 150.193 1 47.22 ? C2 ADP 1602 A 1 HETATM 26 N N3 ADP . . . G 6 164.881 156.462 150.328 1 47.22 ? N3 ADP 1602 A 1 HETATM 27 C C4 ADP . . . G 6 163.673 156.011 149.938 1 47.22 ? C4 ADP 1602 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #