data_1L2O # _model_server_result.job_id YTW-q7XWeOrYtWBCwLgcig _model_server_result.datetime_utc '2024-10-18 16:24:46' _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 1l2o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":999}' # _entry.id 1L2O # _exptl.entry_id 1L2O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _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 95.6 _cell.angle_beta 96.3 _cell.angle_gamma 101.5 _cell.entry_id 1L2O _cell.length_a 51.8 _cell.length_b 57 _cell.length_c 150.5 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1L2O _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,F,G,H,I,J,K _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 6 _struct_asym.id F _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 SG CYS 693 A CYS 693 1_555 E CP9 PDM . A PDM 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.809 ? covale ? covale2 A NZ LYS 705 A LYS 705 1_555 E C13 PDM . A PDM 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 A CE LYS 705 A LYS 705 1_555 E C13 PDM . A PDM 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc1 A OG1 THR 183 A THR 183 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc2 A OG SER 241 A SER 241 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc3 D MG MG . A MG 903 1_555 F O2B ADP . A ADP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc4 D MG MG . A MG 903 1_555 F O3B ADP . A ADP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.975 ? metalc ? metalc5 D MG MG . A MG 903 1_555 I O HOH . A HOH 1016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc6 D MG MG . A MG 903 1_555 I O HOH . A HOH 1017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc7 B OD1 ASP 28 B ASP 28 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc8 B OD2 ASP 30 B ASP 30 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc9 B OD1 ASP 30 B ASP 30 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc10 B N ARG 31 B ARG 31 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc11 B N ASP 32 B ASP 32 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc12 B OD1 ASP 32 B ASP 32 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? metalc ? metalc13 B O PHE 34 B PHE 34 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.127 ? metalc ? metalc14 B OD2 ASP 39 B ASP 39 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc15 C OD1 ASP 19 C ASP 19 1_555 H CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc16 C O ASP 19 C ASP 19 1_555 H CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc17 C OD1 ASP 22 C ASP 22 1_555 H CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc18 C O GLY 23 C GLY 23 1_555 H CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc19 C OD2 ASP 25 C ASP 25 1_555 H CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc20 C OD1 ASP 25 C ASP 25 1_555 H CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.013 ? metalc ? metalc21 C O ALA 27 C ALA 27 1_555 H CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc22 H CA CA . C CA 501 1_555 K O HOH . C HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? # _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 1L2O _atom_sites.fract_transf_matrix[1][1] 0.019305 _atom_sites.fract_transf_matrix[1][2] 0.003928 _atom_sites.fract_transf_matrix[1][3] 0.002633 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017903 _atom_sites.fract_transf_matrix[2][3] 0.002213 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.006736 _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 D 4 MG A 1 903 903 MG MG . E 5 PDM A 1 900 900 PDM PDM . F 6 ADP A 1 999 999 ADP ADP . G 4 MG B 1 902 902 MG MG . H 7 CA C 1 501 501 CA CA . I 8 HOH A 1 1000 616 HOH HOH . I 8 HOH A 2 1001 618 HOH HOH . I 8 HOH A 3 1002 619 HOH HOH . I 8 HOH A 4 1003 620 HOH HOH . I 8 HOH A 5 1004 621 HOH HOH . I 8 HOH A 6 1005 622 HOH HOH . I 8 HOH A 7 1006 623 HOH HOH . I 8 HOH A 8 1007 624 HOH HOH . I 8 HOH A 9 1008 625 HOH HOH . I 8 HOH A 10 1009 626 HOH HOH . I 8 HOH A 11 1010 630 HOH HOH . I 8 HOH A 12 1011 631 HOH HOH . I 8 HOH A 13 1012 632 HOH HOH . I 8 HOH A 14 1013 633 HOH HOH . I 8 HOH A 15 1014 634 HOH HOH . I 8 HOH A 16 1015 635 HOH HOH . I 8 HOH A 17 1016 636 HOH HOH . I 8 HOH A 18 1017 637 HOH HOH . I 8 HOH A 19 1018 638 HOH HOH . I 8 HOH A 20 1019 639 HOH HOH . I 8 HOH A 21 1020 640 HOH HOH . I 8 HOH A 22 1021 641 HOH HOH . I 8 HOH A 23 1022 642 HOH HOH . I 8 HOH A 24 1023 643 HOH HOH . I 8 HOH A 25 1024 644 HOH HOH . J 8 HOH B 1 903 1 HOH HOH . J 8 HOH B 2 904 629 HOH HOH . K 8 HOH C 1 502 16 HOH HOH . K 8 HOH C 2 503 617 HOH HOH . K 8 HOH C 3 504 627 HOH HOH . K 8 HOH C 4 505 628 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 . . . F 6 -3.233 3.61 -3.062 1 81.96 ? PB ADP 999 A 1 HETATM 2 O O1B ADP . . . F 6 -3.139 3.644 -1.567 1 83.67 ? O1B ADP 999 A 1 HETATM 3 O O2B ADP . . . F 6 -2.006 3.289 -3.769 1 85.64 ? O2B ADP 999 A 1 HETATM 4 O O3B ADP . . . F 6 -4.345 2.599 -3.468 1 88.05 ? O3B ADP 999 A 1 HETATM 5 P PA ADP . . . F 6 -2.95 6.305 -4.08 1 81.44 ? PA ADP 999 A 1 HETATM 6 O O1A ADP . . . F 6 -1.65 6.659 -3.535 1 77.32 ? O1A ADP 999 A 1 HETATM 7 O O2A ADP . . . F 6 -2.872 6.014 -5.503 1 83.25 ? O2A ADP 999 A 1 HETATM 8 O O3A ADP . . . F 6 -3.629 5.102 -3.246 1 81.15 ? O3A ADP 999 A 1 HETATM 9 O O5' ADP . . . F 6 -3.951 7.524 -3.878 1 76.36 ? O5' ADP 999 A 1 HETATM 10 C C5' ADP . . . F 6 -5.356 7.659 -4.301 1 80.14 ? C5' ADP 999 A 1 HETATM 11 C C4' ADP . . . F 6 -5.637 9.038 -4.647 1 83.31 ? C4' ADP 999 A 1 HETATM 12 O O4' ADP . . . F 6 -5.701 9.824 -3.419 1 82.4 ? O4' ADP 999 A 1 HETATM 13 C C3' ADP . . . F 6 -4.614 9.783 -5.486 1 82.13 ? C3' ADP 999 A 1 HETATM 14 O O3' ADP . . . F 6 -4.918 9.533 -6.847 1 78.08 ? O3' ADP 999 A 1 HETATM 15 C C2' ADP . . . F 6 -4.844 11.212 -5.057 1 82.39 ? C2' ADP 999 A 1 HETATM 16 O O2' ADP . . . F 6 -5.949 11.858 -5.7 1 86.37 ? O2' ADP 999 A 1 HETATM 17 C C1' ADP . . . F 6 -5.113 11.138 -3.581 1 81.53 ? C1' ADP 999 A 1 HETATM 18 N N9 ADP . . . F 6 -3.858 11.254 -2.761 1 84.12 ? N9 ADP 999 A 1 HETATM 19 C C8 ADP . . . F 6 -3.257 10.317 -1.916 1 85.71 ? C8 ADP 999 A 1 HETATM 20 N N7 ADP . . . F 6 -2.261 10.771 -1.228 1 85.25 ? N7 ADP 999 A 1 HETATM 21 C C5 ADP . . . F 6 -2.163 12.083 -1.684 1 86.9 ? C5 ADP 999 A 1 HETATM 22 C C6 ADP . . . F 6 -1.261 13.143 -1.353 1 86.96 ? C6 ADP 999 A 1 HETATM 23 N N6 ADP . . . F 6 -0.296 12.967 -0.468 1 81.81 ? N6 ADP 999 A 1 HETATM 24 N N1 ADP . . . F 6 -1.42 14.356 -1.976 1 88.51 ? N1 ADP 999 A 1 HETATM 25 C C2 ADP . . . F 6 -2.41 14.506 -2.863 1 86.91 ? C2 ADP 999 A 1 HETATM 26 N N3 ADP . . . F 6 -3.322 13.611 -3.263 1 87.23 ? N3 ADP 999 A 1 HETATM 27 C C4 ADP . . . F 6 -3.129 12.376 -2.615 1 86.95 ? C4 ADP 999 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #