data_4WBB # _model_server_result.job_id z1FKvE96zWeR1zefX1mVtQ _model_server_result.datetime_utc '2024-10-28 11:27:16' _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 4wbb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 4WBB # _exptl.entry_id 4WBB _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 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 4WBB _cell.length_a 150.38 _cell.length_b 213.951 _cell.length_c 61.967 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WBB _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 A C ALA 111 A ALA 111 1_555 A N SEP 112 A SEP 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C SEP 112 A SEP 112 1_555 A N VAL 113 A VAL 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale3 B C PHE 138 B PHE 138 1_555 B N SEP 139 B SEP 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 B C SEP 139 B SEP 139 1_555 B N GLU 140 B GLU 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale5 B C TRP 196 B TRP 196 1_555 B N TPO 197 B TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 B C TPO 197 B TPO 197 1_555 B N LEU 198 B LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale7 B C VAL 337 B VAL 337 1_555 B N SEP 338 B SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale8 B C SEP 338 B SEP 338 1_555 B N ILE 339 B ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 A O3P SEP 112 A SEP 112 1_555 C CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc2 C CA CA . A CA 501 1_555 D O2B ADP . A ADP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc3 C CA CA . A CA 501 1_555 B OD1 ASP 184 B ASP 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc4 C CA CA . A CA 501 1_555 B OD2 ASP 184 B ASP 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc5 C CA CA . A CA 501 1_555 G O HOH . B HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc6 D O2B ADP . A ADP 502 1_555 E CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc7 D O3B ADP . A ADP 502 1_555 E CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.163 ? metalc ? metalc8 D O2A ADP . A ADP 502 1_555 E CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc9 F O HOH . A HOH 607 1_555 E CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc10 B OD1 ASN 171 B ASN 171 1_555 E CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc11 B OD1 ASP 184 B ASP 184 1_555 E CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc12 E CA CA . B CA 401 1_555 G O HOH . B HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? # _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 4WBB _atom_sites.fract_transf_matrix[1][1] 0.00665 _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] 0.004674 _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] 0.016138 _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 1 501 401 CA CA . D 4 ADP A 1 502 400 ADP ADP . E 3 CA B 1 401 402 CA CA . F 5 HOH A 1 601 31 HOH HOH . F 5 HOH A 2 602 6 HOH HOH . F 5 HOH A 3 603 29 HOH HOH . F 5 HOH A 4 604 39 HOH HOH . F 5 HOH A 5 605 42 HOH HOH . F 5 HOH A 6 606 17 HOH HOH . F 5 HOH A 7 607 1 HOH HOH . F 5 HOH A 8 608 2 HOH HOH . F 5 HOH A 9 609 7 HOH HOH . F 5 HOH A 10 610 9 HOH HOH . F 5 HOH A 11 611 11 HOH HOH . F 5 HOH A 12 612 13 HOH HOH . F 5 HOH A 13 613 14 HOH HOH . F 5 HOH A 14 614 15 HOH HOH . F 5 HOH A 15 615 16 HOH HOH . F 5 HOH A 16 616 18 HOH HOH . F 5 HOH A 17 617 19 HOH HOH . F 5 HOH A 18 618 20 HOH HOH . F 5 HOH A 19 619 22 HOH HOH . F 5 HOH A 20 620 24 HOH HOH . F 5 HOH A 21 621 26 HOH HOH . F 5 HOH A 22 622 36 HOH HOH . F 5 HOH A 23 623 37 HOH HOH . F 5 HOH A 24 624 38 HOH HOH . G 5 HOH B 1 501 25 HOH HOH . G 5 HOH B 2 502 30 HOH HOH . G 5 HOH B 3 503 3 HOH HOH . G 5 HOH B 4 504 4 HOH HOH . G 5 HOH B 5 505 5 HOH HOH . G 5 HOH B 6 506 8 HOH HOH . G 5 HOH B 7 507 10 HOH HOH . G 5 HOH B 8 508 12 HOH HOH . G 5 HOH B 9 509 21 HOH HOH . G 5 HOH B 10 510 23 HOH HOH . G 5 HOH B 11 511 27 HOH HOH . G 5 HOH B 12 512 28 HOH HOH . G 5 HOH B 13 513 32 HOH HOH . G 5 HOH B 14 514 33 HOH HOH . G 5 HOH B 15 515 34 HOH HOH . G 5 HOH B 16 516 35 HOH HOH . G 5 HOH B 17 517 40 HOH HOH . G 5 HOH B 18 518 41 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 . . . D 4 30.2 32.218 -8.347 1 44.92 ? PB ADP 502 A 1 HETATM 2 O O1B ADP . . . D 4 30.975 32.011 -9.626 1 45.79 ? O1B ADP 502 A 1 HETATM 3 O O2B ADP . . . D 4 30.64 31.337 -7.202 1 47.85 ? O2B ADP 502 A 1 HETATM 4 O O3B ADP . . . D 4 29.989 33.666 -7.974 1 40.83 ? O3B ADP 502 A 1 HETATM 5 P PA ADP . . . D 4 27.646 31.429 -7.529 1 45.48 ? PA ADP 502 A 1 HETATM 6 O O1A ADP . . . D 4 27.174 29.998 -7.63 1 40.07 ? O1A ADP 502 A 1 HETATM 7 O O2A ADP . . . D 4 28.227 31.94 -6.232 1 42.68 ? O2A ADP 502 A 1 HETATM 8 O O3A ADP . . . D 4 28.721 31.688 -8.699 1 32.95 ? O3A ADP 502 A 1 HETATM 9 O O5' ADP . . . D 4 26.428 32.393 -7.95 1 40.38 ? O5' ADP 502 A 1 HETATM 10 C C5' ADP . . . D 4 26.663 33.549 -8.751 1 36.32 ? C5' ADP 502 A 1 HETATM 11 C C4' ADP . . . D 4 25.665 34.638 -8.377 1 36.45 ? C4' ADP 502 A 1 HETATM 12 O O4' ADP . . . D 4 24.441 34.436 -9.089 1 46.96 ? O4' ADP 502 A 1 HETATM 13 C C3' ADP . . . D 4 25.348 34.608 -6.89 1 40.45 ? C3' ADP 502 A 1 HETATM 14 O O3' ADP . . . D 4 25.706 35.856 -6.288 1 47.96 ? O3' ADP 502 A 1 HETATM 15 C C2' ADP . . . D 4 23.853 34.387 -6.778 1 45.5 ? C2' ADP 502 A 1 HETATM 16 O O2' ADP . . . D 4 23.243 35.491 -6.104 1 41.53 ? O2' ADP 502 A 1 HETATM 17 C C1' ADP . . . D 4 23.329 34.292 -8.202 1 50.58 ? C1' ADP 502 A 1 HETATM 18 N N9 ADP . . . D 4 22.689 32.969 -8.412 1 46.27 ? N9 ADP 502 A 1 HETATM 19 C C8 ADP . . . D 4 23.334 31.808 -8.629 1 43.4 ? C8 ADP 502 A 1 HETATM 20 N N7 ADP . . . D 4 22.459 30.781 -8.782 1 46.66 ? N7 ADP 502 A 1 HETATM 21 C C5 ADP . . . D 4 21.218 31.288 -8.662 1 45.67 ? C5 ADP 502 A 1 HETATM 22 C C6 ADP . . . D 4 19.836 30.754 -8.717 1 47.53 ? C6 ADP 502 A 1 HETATM 23 N N6 ADP . . . D 4 19.602 29.438 -8.937 1 50.67 ? N6 ADP 502 A 1 HETATM 24 N N1 ADP . . . D 4 18.818 31.625 -8.54 1 46.72 ? N1 ADP 502 A 1 HETATM 25 C C2 ADP . . . D 4 19.037 32.935 -8.321 1 47.38 ? C2 ADP 502 A 1 HETATM 26 N N3 ADP . . . D 4 20.263 33.487 -8.259 1 48.4 ? N3 ADP 502 A 1 HETATM 27 C C4 ADP . . . D 4 21.375 32.73 -8.418 1 46.75 ? C4 ADP 502 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #