data_4PU9 # _model_server_result.job_id LBgjTdnNKp1Kl1g3UY3R6A _model_server_result.datetime_utc '2024-11-27 14:11:03' _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 4pu9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4PU9 # _exptl.entry_id 4PU9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 4PU9 _cell.length_a 88.083 _cell.length_b 143.245 _cell.length_c 79.895 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PU9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -39.9475 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 metalc ? metalc1 A OD1 ASN 52 A ASN 46 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc2 B O3B ADP . A ADP 401 1_555 C BE BEF . A BEF 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.593 ? metalc ? metalc3 B O2B ADP . A ADP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc4 B O1A ADP . A ADP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc5 D MG MG . A MG 403 1_555 E O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? # _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 4PU9 _atom_sites.fract_transf_matrix[1][1] 0.011353 _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] 0.006981 _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] 0.012516 _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 B 2 ADP A 1 401 1 ADP ADP . C 3 BEF A 1 402 2 BEF BEF . D 4 MG A 1 403 3 MG MG . E 5 HOH A 1 501 1 HOH HOH . E 5 HOH A 2 502 2 HOH HOH . E 5 HOH A 3 503 3 HOH HOH . E 5 HOH A 4 504 4 HOH HOH . E 5 HOH A 5 505 5 HOH HOH . E 5 HOH A 6 506 7 HOH HOH . E 5 HOH A 7 507 8 HOH HOH . E 5 HOH A 8 508 9 HOH HOH . E 5 HOH A 9 509 10 HOH HOH . E 5 HOH A 10 510 11 HOH HOH . E 5 HOH A 11 511 13 HOH HOH . E 5 HOH A 12 512 15 HOH HOH . E 5 HOH A 13 513 17 HOH HOH . E 5 HOH A 14 514 19 HOH HOH . E 5 HOH A 15 515 20 HOH HOH . E 5 HOH A 16 516 22 HOH HOH . E 5 HOH A 17 517 23 HOH HOH . E 5 HOH A 18 518 24 HOH HOH . E 5 HOH A 19 519 25 HOH HOH . E 5 HOH A 20 520 26 HOH HOH . E 5 HOH A 21 521 27 HOH HOH . E 5 HOH A 22 522 30 HOH HOH . E 5 HOH A 23 523 31 HOH HOH . E 5 HOH A 24 524 32 HOH HOH . E 5 HOH A 25 525 33 HOH HOH . E 5 HOH A 26 526 34 HOH HOH . E 5 HOH A 27 527 35 HOH HOH . E 5 HOH A 28 528 36 HOH HOH . E 5 HOH A 29 529 37 HOH HOH . E 5 HOH A 30 530 41 HOH HOH . E 5 HOH A 31 531 42 HOH HOH . E 5 HOH A 32 532 43 HOH HOH . E 5 HOH A 33 533 44 HOH HOH . E 5 HOH A 34 534 45 HOH HOH . E 5 HOH A 35 535 46 HOH HOH . E 5 HOH A 36 536 47 HOH HOH . E 5 HOH A 37 537 49 HOH HOH . E 5 HOH A 38 538 50 HOH HOH . E 5 HOH A 39 539 52 HOH HOH . E 5 HOH A 40 540 54 HOH HOH . E 5 HOH A 41 541 56 HOH HOH . E 5 HOH A 42 542 57 HOH HOH . E 5 HOH A 43 543 58 HOH HOH . E 5 HOH A 44 544 60 HOH HOH . E 5 HOH A 45 545 62 HOH HOH . E 5 HOH A 46 546 63 HOH HOH . E 5 HOH A 47 547 64 HOH HOH . E 5 HOH A 48 548 65 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 . . . B 2 -9.428 21.727 -28.204 1 27.34 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -8.995 20.648 -29.177 1 26.69 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -10.639 22.555 -28.609 1 27.61 -1 O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -8.195 22.428 -27.607 1 29.84 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -10.957 20.665 -25.885 1 29.86 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -11.797 21.835 -25.514 1 30.59 -1 O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -10.348 19.84 -24.787 1 30.38 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -9.693 21.109 -26.758 1 26.71 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -11.715 19.628 -26.83 1 32.49 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -11.045 18.612 -27.526 1 28.72 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -11.898 18.295 -28.713 1 30.02 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -13.232 18.012 -28.335 1 32.37 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -12.101 19.377 -29.73 1 32.53 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -10.929 19.644 -30.489 1 33.24 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -13.256 18.802 -30.554 1 34.78 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -12.787 17.826 -31.487 1 35.38 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -14.089 18.134 -29.482 1 31.77 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -15.199 19.006 -29.079 1 30.94 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -15.267 19.718 -27.934 1 30.82 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -16.447 20.393 -27.863 1 30.21 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -17.148 20.073 -28.946 1 28.4 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -18.442 20.459 -29.51 1 32.22 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -19.267 21.312 -28.831 1 32.76 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -18.776 19.893 -30.698 1 31.17 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -17.974 19.071 -31.359 1 28.24 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -16.762 18.749 -30.922 1 26.47 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -16.312 19.193 -29.757 1 28.31 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #