data_1RPZ # _model_server_result.job_id gsrf1oVSacOeCFx1tt7Yuw _model_server_result.datetime_utc '2024-12-22 01:11:15' _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 1rpz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":900}' # _entry.id 1RPZ # _exptl.entry_id 1RPZ _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 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 1RPZ _cell.length_a 80.565 _cell.length_b 92.633 _cell.length_c 122.665 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RPZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 80.565 92.633 0 3 'crystal symmetry operation' 3_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 80.565 0 122.665 4 'crystal symmetry operation' 4_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 92.633 122.665 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 B C MSE 1 A MSE 1 1_555 B N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 B C ILE 41 A ILE 41 1_555 B N MSE 42 A MSE 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 B C MSE 42 A MSE 42 1_555 B N ALA 43 A ALA 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 B C GLY 62 A GLY 62 1_555 B N MSE 63 A MSE 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 B C MSE 63 A MSE 63 1_555 B N GLN 64 A GLN 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 B C SER 138 A SER 138 1_555 B N MSE 139 A MSE 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale7 B C MSE 139 A MSE 139 1_555 B N TYR 140 A TYR 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale8 B C SER 142 A SER 142 1_555 B N MSE 143 A MSE 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale9 B C MSE 143 A MSE 143 1_555 B N ARG 144 A ARG 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 B C LYS 172 A LYS 172 1_555 B N MSE 173 A MSE 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale11 B C PRO 191 A PRO 191 1_555 B N MSE 192 A MSE 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale12 B C MSE 192 A MSE 192 1_555 B N VAL 193 A VAL 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale13 B C LYS 198 A LYS 198 1_555 B N MSE 199 A MSE 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale14 B C MSE 199 A MSE 199 1_555 B N TYR 200 A TYR 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale15 B C LEU 202 A LEU 202 1_555 B N MSE 203 A MSE 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale16 B C MSE 203 A MSE 203 1_555 B N GLY 204 A GLY 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale17 B C ARG 226 A ARG 226 1_555 B N MSE 227 A MSE 227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale18 B C MSE 227 A MSE 227 1_555 B N THR 228 A THR 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale19 B C VAL 241 A VAL 241 1_555 B N MSE 242 A MSE 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale20 B C MSE 242 A MSE 242 1_555 B N GLN 243 A GLN 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale21 B C GLU 284 A GLU 284 1_555 B N MSE 285 A MSE 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale22 B C MSE 285 A MSE 285 1_555 B N TRP 286 A TRP 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 B OD1 ASP 165 A ASP 165 1_555 C CA CA . A CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc2 B O ASP 167 A ASP 167 1_555 C CA CA . A CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc3 B OD1 ASP 278 A ASP 278 1_555 C CA CA . A CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? # _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 1RPZ _atom_sites.fract_transf_matrix[1][1] 0.012412 _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] 0.010795 _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] 0.008152 _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 CA A 1 700 700 CA CA . D 4 DMS A 1 800 800 DMS DMS . E 4 DMS A 1 801 801 DMS DMS . F 5 ADP A 1 900 900 ADP ADP . G 6 HOH B 1 503 503 HOH HOH . H 6 HOH A 1 500 500 HOH HOH . H 6 HOH A 2 501 501 HOH HOH . H 6 HOH A 3 502 502 HOH HOH . H 6 HOH A 4 504 504 HOH HOH . H 6 HOH A 5 505 505 HOH HOH . H 6 HOH A 6 506 506 HOH HOH . H 6 HOH A 7 507 507 HOH HOH . H 6 HOH A 8 508 508 HOH HOH . H 6 HOH A 9 509 509 HOH HOH . H 6 HOH A 10 510 510 HOH HOH . H 6 HOH A 11 511 511 HOH HOH . H 6 HOH A 12 512 512 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 PB ADP . . . F 5 29.514 55.186 51.145 1 122.71 ? PB ADP 900 A 1 HETATM 2 O O1B ADP . . . F 5 28.278 54.699 51.803 1 122.71 ? O1B ADP 900 A 1 HETATM 3 O O2B ADP . . . F 5 30.375 53.949 50.627 1 122.71 ? O2B ADP 900 A 1 HETATM 4 O O3B ADP . . . F 5 29.193 56.096 50.01 1 122.71 ? O3B ADP 900 A 1 HETATM 5 P PA ADP . . . F 5 32.001 56.192 52.245 1 122.71 ? PA ADP 900 A 1 HETATM 6 O O1A ADP . . . F 5 32.554 56.14 50.892 1 122.71 ? O1A ADP 900 A 1 HETATM 7 O O2A ADP . . . F 5 32.281 57.509 52.812 1 122.71 ? O2A ADP 900 A 1 HETATM 8 O O3A ADP . . . F 5 30.442 55.921 52.196 1 122.71 ? O3A ADP 900 A 1 HETATM 9 O O5' ADP . . . F 5 32.699 55.083 53.185 1 122.71 ? O5' ADP 900 A 1 HETATM 10 C C5' ADP . . . F 5 32.094 53.992 53.918 1 122.71 ? C5' ADP 900 A 1 HETATM 11 C C4' ADP . . . F 5 33.258 53.203 54.643 1 122.71 ? C4' ADP 900 A 1 HETATM 12 O O4' ADP . . . F 5 34.18 52.759 53.636 1 122.71 ? O4' ADP 900 A 1 HETATM 13 C C3' ADP . . . F 5 34.117 54.007 55.659 1 122.71 ? C3' ADP 900 A 1 HETATM 14 O O3' ADP . . . F 5 34.291 53.309 56.912 1 122.71 ? O3' ADP 900 A 1 HETATM 15 C C2' ADP . . . F 5 35.458 54.28 54.975 1 122.71 ? C2' ADP 900 A 1 HETATM 16 O O2' ADP . . . F 5 36.57 54.341 55.886 1 122.71 ? O2' ADP 900 A 1 HETATM 17 C C1' ADP . . . F 5 35.539 53.188 53.91 1 122.71 ? C1' ADP 900 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 17 #