data_3D54 # _model_server_result.job_id vRMLTwaMPu1fhv4lhuYSpg _model_server_result.datetime_utc '2025-04-09 15:25:38' _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 3d54 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":2004}' # _entry.id 3D54 # _exptl.entry_id 3D54 _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 99.12 _cell.angle_gamma 90 _cell.entry_id 3D54 _cell.length_a 256.851 _cell.length_b 187.337 _cell.length_c 159.177 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D54 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 PISA tetrameric 4 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression I,J,K,L,Q,R 1 1 E,F,G,H,O,P 2 1 A,B,C,D,M,N 3 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 N N N ? 5 P N N ? 5 R 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 D C ILE 85 D ILE 85 1_555 D N CYG 86 D CYG 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale2 D C CYG 86 D CYG 86 1_555 D N ASN 87 D ASN 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale3 H C ILE 85 H ILE 85 1_555 H N CYG 86 H CYG 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale4 H C CYG 86 H CYG 86 1_555 H N ASN 87 H ASN 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 L C ILE 85 L ILE 85 1_555 L N CYG 86 L CYG 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale6 L C CYG 86 L CYG 86 1_555 L N ASN 87 L ASN 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A OD2 ASP 120 A ASP 94 1_555 M NA NA . A NA 3003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc2 A OD1 ASP 262 A ASP 236 1_555 M NA NA . A NA 3003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc3 A OD2 ASP 262 A ASP 236 1_555 M NA NA . A NA 3003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.183 ? metalc ? metalc4 E OD2 ASP 120 E ASP 94 1_555 O NA NA . E NA 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? metalc ? metalc5 E OD1 ASP 262 E ASP 236 1_555 O NA NA . E NA 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.807 ? metalc ? metalc6 E OD2 ASP 262 E ASP 236 1_555 O NA NA . E NA 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.155 ? metalc ? metalc7 I OD2 ASP 120 I ASP 94 1_555 Q NA NA . I NA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.777 ? metalc ? metalc8 I OD1 ASP 262 I ASP 236 1_555 Q NA NA . I NA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.777 ? metalc ? metalc9 I OD2 ASP 262 I ASP 236 1_555 Q NA NA . I NA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.162 ? # _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 3D54 _atom_sites.fract_transf_matrix[1][1] 0.003893 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000625 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005338 _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] 0.006363 _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 M 4 NA A 1 3003 3003 NA NA . N 5 ADP A 1 2004 2004 ADP ADP . O 4 NA E 1 3002 3002 NA NA . P 5 ADP E 1 2006 2006 ADP ADP . Q 4 NA I 1 3001 3001 NA NA . R 5 ADP I 1 2005 2005 ADP ADP . # 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 . . . N 5 34.703 40.498 9.208 1 162.1 ? PB ADP 2004 A 1 HETATM 2 O O1B ADP . . . N 5 36.084 41.163 8.72 1 170.65 ? O1B ADP 2004 A 1 HETATM 3 O O2B ADP . . . N 5 34.848 39.085 9.623 1 169.19 ? O2B ADP 2004 A 1 HETATM 4 O O3B ADP . . . N 5 34.155 41.44 10.391 1 167.88 ? O3B ADP 2004 A 1 HETATM 5 P PA ADP . . . N 5 32.159 41.087 8.358 1 166.38 ? PA ADP 2004 A 1 HETATM 6 O O1A ADP . . . N 5 31.928 40.725 9.774 1 172.97 ? O1A ADP 2004 A 1 HETATM 7 O O2A ADP . . . N 5 31.277 40.497 7.326 1 165.43 ? O2A ADP 2004 A 1 HETATM 8 O O3A ADP . . . N 5 33.673 40.699 7.991 1 166.59 ? O3A ADP 2004 A 1 HETATM 9 O O5' ADP . . . N 5 32.178 42.689 8.209 1 170.73 ? O5' ADP 2004 A 1 HETATM 10 C C5' ADP . . . N 5 32.799 43.495 9.212 1 177.93 ? C5' ADP 2004 A 1 HETATM 11 C C4' ADP . . . N 5 32.729 44.976 8.838 1 171.86 ? C4' ADP 2004 A 1 HETATM 12 O O4' ADP . . . N 5 31.355 45.393 8.903 1 168.93 ? O4' ADP 2004 A 1 HETATM 13 C C3' ADP . . . N 5 33.424 45.771 9.942 1 186.42 ? C3' ADP 2004 A 1 HETATM 14 O O3' ADP . . . N 5 33.516 47.142 9.551 1 168.55 ? O3' ADP 2004 A 1 HETATM 15 C C2' ADP . . . N 5 32.353 45.635 11.018 1 306.71 ? C2' ADP 2004 A 1 HETATM 16 O O2' ADP . . . N 5 32.569 46.623 12.027 1 171.95 ? O2' ADP 2004 A 1 HETATM 17 C C1' ADP . . . N 5 31.162 46.06 10.161 1 192.26 ? C1' ADP 2004 A 1 HETATM 18 N N9 ADP . . . N 5 29.913 45.632 10.821 1 167.42 ? N9 ADP 2004 A 1 HETATM 19 C C8 ADP . . . N 5 29.42 44.397 10.821 1 181.94 ? C8 ADP 2004 A 1 HETATM 20 N N7 ADP . . . N 5 28.316 44.361 11.563 1 161.2 ? N7 ADP 2004 A 1 HETATM 21 C C5 ADP . . . N 5 28.102 45.582 12.038 1 170.14 ? C5 ADP 2004 A 1 HETATM 22 C C6 ADP . . . N 5 27.139 46.14 12.868 1 161.89 ? C6 ADP 2004 A 1 HETATM 23 N N6 ADP . . . N 5 26.167 45.389 13.374 1 161.27 ? N6 ADP 2004 A 1 HETATM 24 N N1 ADP . . . N 5 27.222 47.441 13.169 1 164.26 ? N1 ADP 2004 A 1 HETATM 25 C C2 ADP . . . N 5 28.202 48.187 12.691 1 166.33 ? C2 ADP 2004 A 1 HETATM 26 N N3 ADP . . . N 5 29.138 47.689 11.903 1 161.08 ? N3 ADP 2004 A 1 HETATM 27 C C4 ADP . . . N 5 29.117 46.396 11.56 1 162.86 ? C4 ADP 2004 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 452 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #