data_7DRP # _model_server_result.job_id O6SDtjseoIV6sW1QE_nEXA _model_server_result.datetime_utc '2025-02-05 16:53:01' _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 7drp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":401}' # _entry.id 7DRP # _exptl.entry_id 7DRP _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-5'-DIPHOSPHATE" _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 101.31 _cell.angle_gamma 90 _cell.entry_id 7DRP _cell.length_a 89.587 _cell.length_b 91.656 _cell.length_c 98.198 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DRP _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,F,G,H,I,J,K,L,S,T 1 1 C,D,E,M,N,O,P,Q,R,U,V 2 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 ? 3 G N N ? 3 J N N ? 3 M N N ? 3 P 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 E C GLY 23 F GLY 23 1_555 E N DV9 24 F DV9 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale2 E C DV9 24 F DV9 24 1_555 E N GLU 25 F GLU 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.311 ? covale ? covale3 F C GLY 23 E GLY 23 1_555 F N DV9 24 E DV9 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale4 F C DV9 24 E DV9 24 1_555 F N GLU 25 E GLU 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.296 ? metalc ? metalc1 A OD2 ASP 289 A ASP 269 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc2 A OE2 GLU 302 A GLU 282 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc3 A OE1 GLU 302 A GLU 282 1_555 I MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc4 A OE2 GLU 302 A GLU 282 1_555 I MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc5 A OD1 ASN 304 A ASN 284 1_555 I MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc6 G O2B ADP . A ADP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc7 G O1A ADP . A ADP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc8 G O1B ADP . A ADP 401 1_555 I MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.898 ? metalc ? metalc9 B OD2 ASP 289 B ASP 269 1_555 K MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc10 B OE2 GLU 302 B GLU 282 1_555 K MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? metalc ? metalc11 B OE1 GLU 302 B GLU 282 1_555 L MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc12 B OE2 GLU 302 B GLU 282 1_555 L MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc13 B OD1 ASN 304 B ASN 284 1_555 L MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc14 J O3B ADP . B ADP 401 1_555 K MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? metalc ? metalc15 J O2A ADP . B ADP 401 1_555 K MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc16 J O2B ADP . B ADP 401 1_555 L MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc17 C OD2 ASP 289 C ASP 269 1_555 N MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc18 C OE1 GLU 302 C GLU 282 1_555 N MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? metalc ? metalc19 C OE2 GLU 302 C GLU 282 1_555 O MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc20 C OD1 ASN 304 C ASN 284 1_555 O MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.761 ? metalc ? metalc21 M O3B ADP . C ADP 401 1_555 N MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc22 M O2A ADP . C ADP 401 1_555 N MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc23 M O1B ADP . C ADP 401 1_555 O MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc24 D OD2 ASP 289 D ASP 269 1_555 Q MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc25 D OE2 GLU 302 D GLU 282 1_555 Q MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc26 D OE1 GLU 302 D GLU 282 1_555 R MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc27 D OE2 GLU 302 D GLU 282 1_555 R MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc28 P O1B ADP . D ADP 401 1_555 Q MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc29 P O1A ADP . D ADP 401 1_555 Q MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc30 P O3B ADP . D ADP 401 1_555 R MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? # _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 7DRP _atom_sites.fract_transf_matrix[1][1] 0.011162 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002233 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01091 _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] 0.010385 _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 3 ADP A 1 401 401 ADP ADP . H 4 MG A 1 402 402 MG MG . I 4 MG A 1 403 403 MG MG . J 3 ADP B 1 401 401 ADP ADP . K 4 MG B 1 402 402 MG MG . L 4 MG B 1 403 403 MG MG . M 3 ADP C 1 401 401 ADP ADP . N 4 MG C 1 402 402 MG MG . O 4 MG C 1 403 403 MG MG . P 3 ADP D 1 401 401 ADP ADP . Q 4 MG D 1 402 402 MG MG . R 4 MG D 1 403 403 MG MG . S 5 HOH A 1 501 9 HOH HOH . S 5 HOH A 2 502 5 HOH HOH . S 5 HOH A 3 503 3 HOH HOH . S 5 HOH A 4 504 1 HOH HOH . S 5 HOH A 5 505 8 HOH HOH . S 5 HOH A 6 506 2 HOH HOH . T 5 HOH B 1 501 10 HOH HOH . U 5 HOH C 1 501 11 HOH HOH . U 5 HOH C 2 502 12 HOH HOH . V 5 HOH D 1 501 7 HOH HOH . V 5 HOH D 2 502 14 HOH HOH . V 5 HOH D 3 503 6 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 . . . P 3 -53.746 9.668 -9.351 1 77.34 ? PB ADP 401 D 1 HETATM 2 O O1B ADP . . . P 3 -53.774 8.443 -10.225 1 78.24 ? O1B ADP 401 D 1 HETATM 3 O O2B ADP . . . P 3 -54.502 9.558 -8.059 1 77.74 ? O2B ADP 401 D 1 HETATM 4 O O3B ADP . . . P 3 -52.359 10.219 -9.18 1 76.25 ? O3B ADP 401 D 1 HETATM 5 P PA ADP . . . P 3 -55.752 10.607 -11.173 1 77.53 ? PA ADP 401 D 1 HETATM 6 O O1A ADP . . . P 3 -55.309 9.727 -12.3 1 78.24 ? O1A ADP 401 D 1 HETATM 7 O O2A ADP . . . P 3 -56.295 11.956 -11.518 1 80.12 ? O2A ADP 401 D 1 HETATM 8 O O3A ADP . . . P 3 -54.535 10.826 -10.143 1 76.83 ? O3A ADP 401 D 1 HETATM 9 O O5' ADP . . . P 3 -56.881 9.812 -10.364 1 76.78 ? O5' ADP 401 D 1 HETATM 10 C C5' ADP . . . P 3 -57.07 8.438 -10.679 1 75.68 ? C5' ADP 401 D 1 HETATM 11 C C4' ADP . . . P 3 -58.536 8.074 -10.708 1 76.93 ? C4' ADP 401 D 1 HETATM 12 O O4' ADP . . . P 3 -59.328 9.169 -10.277 1 77.86 ? O4' ADP 401 D 1 HETATM 13 C C3' ADP . . . P 3 -58.994 7.789 -12.115 1 78.12 ? C3' ADP 401 D 1 HETATM 14 O O3' ADP . . . P 3 -58.968 6.389 -12.381 1 80.07 ? O3' ADP 401 D 1 HETATM 15 C C2' ADP . . . P 3 -60.42 8.276 -12.13 1 79.86 ? C2' ADP 401 D 1 HETATM 16 O O2' ADP . . . P 3 -61.298 7.157 -12.058 1 81.03 ? O2' ADP 401 D 1 HETATM 17 C C1' ADP . . . P 3 -60.6 9.135 -10.912 1 79.94 ? C1' ADP 401 D 1 HETATM 18 N N9 ADP . . . P 3 -60.929 10.479 -11.402 1 81.04 ? N9 ADP 401 D 1 HETATM 19 C C8 ADP . . . P 3 -60.02 11.418 -11.652 1 78.66 ? C8 ADP 401 D 1 HETATM 20 N N7 ADP . . . P 3 -60.6 12.543 -12.111 1 77.75 ? N7 ADP 401 D 1 HETATM 21 C C5 ADP . . . P 3 -61.911 12.327 -12.156 1 80.46 ? C5 ADP 401 D 1 HETATM 22 C C6 ADP . . . P 3 -63.078 13.121 -12.55 1 82.99 ? C6 ADP 401 D 1 HETATM 23 N N6 ADP . . . P 3 -62.919 14.388 -12.975 1 83.94 ? N6 ADP 401 D 1 HETATM 24 N N1 ADP . . . P 3 -64.282 12.54 -12.453 1 85.29 ? N1 ADP 401 D 1 HETATM 25 C C2 ADP . . . P 3 -64.419 11.281 -12.019 1 86.33 ? C2 ADP 401 D 1 HETATM 26 N N3 ADP . . . P 3 -63.397 10.497 -11.647 1 85.02 ? N3 ADP 401 D 1 HETATM 27 C C4 ADP . . . P 3 -62.132 10.96 -11.693 1 82.33 ? C4 ADP 401 D 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 27 #