data_6YCX # _model_server_result.job_id 33j2W6XMM6Xe70VuqUUUXQ _model_server_result.datetime_utc '2024-11-04 20:52:21' _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 6ycx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":901}' # _entry.id 6YCX # _exptl.entry_id 6YCX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 6YCX _cell.length_a 168.24 _cell.length_b 287.43 _cell.length_c 78.61 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YCX _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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,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 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 ? 5 G N N ? 5 J 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 covale ? covale1 A C VAL 18 A VAL 18 1_555 A N SEP 19 A SEP 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 ? covale ? covale2 A C SEP 19 A SEP 19 1_555 A N ASN 20 A ASN 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.36 ? covale ? covale3 B C VAL 18 B VAL 18 1_555 B N SEP 19 B SEP 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale4 B C SEP 19 B SEP 19 1_555 B N ASN 20 B ASN 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? metalc ? metalc1 A OG1 THR 198 A THR 198 1_555 I MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc2 A OG SER 246 A SER 246 1_555 I MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc3 G O1B ADP . A ADP 901 1_555 I MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc4 G O2B ADP . A ADP 901 1_555 I MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.931 ? metalc ? metalc5 H O2 VO4 . A VO4 902 1_555 I MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc6 J O3B ADP . B ADP 901 1_555 L MG MG . B MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? # _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 6YCX _atom_sites.fract_transf_matrix[1][1] 0.005944 _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] 0.003479 _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] 0.012721 _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 G 5 ADP A 1 901 901 ADP ADP . H 6 VO4 A 1 902 1001 VO4 VO4 . I 7 MG A 1 903 1 MG MG . J 5 ADP B 1 901 901 ADP ADP . K 6 VO4 B 1 902 1001 VO4 VO4 . L 7 MG B 1 903 2 MG MG . # 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 . . . J 5 50.821 336.552 -65.841 1 36.09 ? PB ADP 901 B 1 HETATM 2 O O1B ADP . . . J 5 50.134 335.869 -67.008 1 41.35 ? O1B ADP 901 B 1 HETATM 3 O O2B ADP . . . J 5 50.077 337.869 -65.557 1 35.83 -1 O2B ADP 901 B 1 HETATM 4 O O3B ADP . . . J 5 52.267 336.757 -66.112 1 37.01 ? O3B ADP 901 B 1 HETATM 5 P PA ADP . . . J 5 50.313 335.75 -63.049 1 38.99 ? PA ADP 901 B 1 HETATM 6 O O1A ADP . . . J 5 49.141 336.724 -62.867 1 41.17 ? O1A ADP 901 B 1 HETATM 7 O O2A ADP . . . J 5 51.518 336.326 -62.409 1 35.26 -1 O2A ADP 901 B 1 HETATM 8 O O3A ADP . . . J 5 50.578 335.563 -64.611 1 39.51 ? O3A ADP 901 B 1 HETATM 9 O O5' ADP . . . J 5 49.902 334.341 -62.385 1 40.19 ? O5' ADP 901 B 1 HETATM 10 C C5' ADP . . . J 5 48.853 333.464 -62.846 1 42.85 ? C5' ADP 901 B 1 HETATM 11 C C4' ADP . . . J 5 48.628 332.371 -61.827 1 42.89 ? C4' ADP 901 B 1 HETATM 12 O O4' ADP . . . J 5 49.875 331.701 -61.55 1 40.14 ? O4' ADP 901 B 1 HETATM 13 C C3' ADP . . . J 5 48.103 332.841 -60.475 1 43.44 ? C3' ADP 901 B 1 HETATM 14 O O3' ADP . . . J 5 46.679 332.915 -60.497 1 44.59 ? O3' ADP 901 B 1 HETATM 15 C C2' ADP . . . J 5 48.654 331.788 -59.498 1 41.1 ? C2' ADP 901 B 1 HETATM 16 O O2' ADP . . . J 5 47.768 330.696 -59.264 1 42.6 ? O2' ADP 901 B 1 HETATM 17 C C1' ADP . . . J 5 49.942 331.313 -60.189 1 37.42 ? C1' ADP 901 B 1 HETATM 18 N N9 ADP . . . J 5 51.186 331.822 -59.611 1 37.08 ? N9 ADP 901 B 1 HETATM 19 C C8 ADP . . . J 5 52.057 332.721 -60.17 1 36.03 ? C8 ADP 901 B 1 HETATM 20 N N7 ADP . . . J 5 53.15 332.914 -59.473 1 35.32 ? N7 ADP 901 B 1 HETATM 21 C C5 ADP . . . J 5 52.981 332.098 -58.364 1 35.52 ? C5 ADP 901 B 1 HETATM 22 C C6 ADP . . . J 5 53.78 331.866 -57.223 1 33.74 ? C6 ADP 901 B 1 HETATM 23 N N6 ADP . . . J 5 54.978 332.427 -57.026 1 31.02 ? N6 ADP 901 B 1 HETATM 24 N N1 ADP . . . J 5 53.297 331.023 -56.28 1 35.88 ? N1 ADP 901 B 1 HETATM 25 C C2 ADP . . . J 5 52.102 330.452 -56.477 1 36.51 ? C2 ADP 901 B 1 HETATM 26 N N3 ADP . . . J 5 51.273 330.576 -57.519 1 35.79 ? N3 ADP 901 B 1 HETATM 27 C C4 ADP . . . J 5 51.771 331.423 -58.432 1 36.88 ? C4 ADP 901 B 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #