data_2XAL # _model_server_result.job_id Gj7PLXeL0kGUqtMTGv2-gQ _model_server_result.datetime_utc '2024-11-23 11:42:02' _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 2xal # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":600}' # _entry.id 2XAL # _exptl.entry_id 2XAL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 2XAL _cell.length_a 58.063 _cell.length_b 110.971 _cell.length_c 138.694 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XAL _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,E,F,G 1 1 B,H,I,J,K,L 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 ? 4 F N N ? 4 K 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 disulf ? disulf1 B SG CYS 330 B CYS 330 1_555 B SG CYS 333 B CYS 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc1 A ND1 HIS 320 A HIS 320 1_555 G ZN ZN . A ZN 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc2 A SG CYS 330 A CYS 330 1_555 G ZN ZN . A ZN 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc3 A SG CYS 333 A CYS 333 1_555 G ZN ZN . A ZN 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc4 A NE2 HIS 346 A HIS 346 1_555 G ZN ZN . A ZN 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc5 A OD2 ASP 407 A ASP 407 1_555 D PB PB . A PB 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc6 A OD1 ASP 407 A ASP 407 1_555 E PB PB . A PB 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc7 A OD2 ASP 407 A ASP 407 1_555 E PB PB . A PB 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? metalc ? metalc8 A OG SER 409 A SER 409 1_555 E PB PB . A PB 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.076 ? metalc ? metalc9 C O23 IHP . A IHP 500 1_555 D PB PB . A PB 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.007 ? metalc ? metalc10 C O43 IHP . A IHP 500 1_555 D PB PB . A PB 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? metalc ? metalc11 C O43 IHP . A IHP 500 1_555 E PB PB . A PB 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc12 D PB PB . A PB 501 1_555 F O2B ADP . A ADP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.126 ? metalc ? metalc13 D PB PB . A PB 501 1_555 F O3B ADP . A ADP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? metalc ? metalc14 D PB PB . A PB 501 1_555 F O2A ADP . A ADP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc15 E PB PB . A PB 502 1_555 F O2B ADP . A ADP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc16 B ND1 HIS 320 B HIS 320 1_555 L ZN ZN . B ZN 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc17 B SG CYS 330 B CYS 330 1_555 L ZN ZN . B ZN 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc18 B NE2 HIS 346 B HIS 346 1_555 L ZN ZN . B ZN 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.733 ? metalc ? metalc19 B OD2 ASP 407 B ASP 407 1_555 I PB PB . B PB 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc20 B OD1 ASP 407 B ASP 407 1_555 J PB PB . B PB 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc21 B OD2 ASP 407 B ASP 407 1_555 J PB PB . B PB 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc22 B OG SER 409 B SER 409 1_555 J PB PB . B PB 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc23 H O23 IHP . B IHP 500 1_555 I PB PB . B PB 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc24 H O43 IHP . B IHP 500 1_555 J PB PB . B PB 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc25 I PB PB . B PB 503 1_555 K O1B ADP . B ADP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc26 I PB PB . B PB 503 1_555 K O1A ADP . B ADP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc27 J PB PB . B PB 504 1_555 K O2B ADP . B ADP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? metalc ? metalc28 J PB PB . B PB 504 1_555 K O1B ADP . B ADP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? # _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 2XAL _atom_sites.fract_transf_matrix[1][1] 0.017223 _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] 0.009011 _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] 0.00721 _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 2 IHP A 1 500 500 IHP I6P . D 3 PB A 1 501 501 PB PB . E 3 PB A 1 502 502 PB PB . F 4 ADP A 1 600 600 ADP ADP . G 5 ZN A 1 700 700 ZN ZN . H 2 IHP B 1 500 500 IHP I6P . I 3 PB B 1 503 503 PB PB . J 3 PB B 1 504 504 PB PB . K 4 ADP B 1 600 600 ADP ADP . L 5 ZN B 1 700 700 ZN ZN . # 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 . . . K 4 67.66 51.372 71.14 1 11.01 ? PB ADP 600 B 1 HETATM 2 O O1B ADP . . . K 4 66.782 51.535 69.916 1 9.51 ? O1B ADP 600 B 1 HETATM 3 O O2B ADP . . . K 4 67.019 52.127 72.29 1 10.05 ? O2B ADP 600 B 1 HETATM 4 O O3B ADP . . . K 4 69.157 51.641 70.909 1 9.98 ? O3B ADP 600 B 1 HETATM 5 P PA ADP . . . K 4 66.191 49.117 72.043 1 8.41 ? PA ADP 600 B 1 HETATM 6 O O1A ADP . . . K 4 65.276 49.153 70.85 1 10.42 ? O1A ADP 600 B 1 HETATM 7 O O2A ADP . . . K 4 65.706 49.714 73.363 1 8.86 ? O2A ADP 600 B 1 HETATM 8 O O3A ADP . . . K 4 67.586 49.784 71.554 1 8.51 ? O3A ADP 600 B 1 HETATM 9 O O5' ADP . . . K 4 66.381 47.568 72.363 1 6.5 ? O5' ADP 600 B 1 HETATM 10 C C5' ADP . . . K 4 67.545 46.865 72.002 1 6.03 ? C5' ADP 600 B 1 HETATM 11 C C4' ADP . . . K 4 66.971 45.494 71.707 1 8.22 ? C4' ADP 600 B 1 HETATM 12 O O4' ADP . . . K 4 66.844 44.725 72.9 1 7.89 ? O4' ADP 600 B 1 HETATM 13 C C3' ADP . . . K 4 65.549 45.521 71.128 1 8.3 ? C3' ADP 600 B 1 HETATM 14 O O3' ADP . . . K 4 65.492 45.664 69.699 1 11.38 ? O3' ADP 600 B 1 HETATM 15 C C2' ADP . . . K 4 65.062 44.138 71.427 1 6.83 ? C2' ADP 600 B 1 HETATM 16 O O2' ADP . . . K 4 65.639 43.295 70.436 1 4.31 ? O2' ADP 600 B 1 HETATM 17 C C1' ADP . . . K 4 65.698 43.888 72.766 1 8.07 ? C1' ADP 600 B 1 HETATM 18 N N9 ADP . . . K 4 64.788 44.409 73.784 1 10.11 ? N9 ADP 600 B 1 HETATM 19 C C8 ADP . . . K 4 64.579 45.71 74.109 1 11.53 ? C8 ADP 600 B 1 HETATM 20 N N7 ADP . . . K 4 63.665 45.825 75.115 1 10.22 ? N7 ADP 600 B 1 HETATM 21 C C5 ADP . . . K 4 63.305 44.567 75.42 1 9.12 ? C5 ADP 600 B 1 HETATM 22 C C6 ADP . . . K 4 62.406 43.961 76.391 1 8.83 ? C6 ADP 600 B 1 HETATM 23 N N6 ADP . . . K 4 61.715 44.748 77.234 1 8.93 ? N6 ADP 600 B 1 HETATM 24 N N1 ADP . . . K 4 62.323 42.617 76.395 1 9.83 ? N1 ADP 600 B 1 HETATM 25 C C2 ADP . . . K 4 63.045 41.829 75.553 1 10.47 ? C2 ADP 600 B 1 HETATM 26 N N3 ADP . . . K 4 63.89 42.3 74.629 1 9.41 ? N3 ADP 600 B 1 HETATM 27 C C4 ADP . . . K 4 64.041 43.64 74.543 1 9.7 ? C4 ADP 600 B 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #