data_7DBB # _model_server_result.job_id mrrVrKzKOoZPBNnhiaS4og _model_server_result.datetime_utc '2024-11-22 23:55:27' _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 7dbb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":401}' # _entry.id 7DBB # _exptl.entry_id 7DBB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 7DBB _cell.length_a 105 _cell.length_b 157.573 _cell.length_c 181.629 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DBB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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,L,M,N,O,P,Q,R,S,T,U,V,W _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 11 _struct_asym.id W _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 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.851 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc10 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc11 B OE1 GLU 111 B GLU 113 1_555 M CA CA . B CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc12 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc13 C OD1 ASP 39 C ASP 39 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc14 C OD2 ASP 39 C ASP 39 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc15 C O THR 41 C THR 41 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc16 C OG1 THR 41 C THR 41 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc17 C O GLY 44 C GLY 44 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc18 C OE1 GLU 55 C GLU 55 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc19 R O1G GTP . C GTP 501 1_555 S MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc20 R O1B GTP . C GTP 501 1_555 S MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? metalc ? metalc21 U MG MG . D MG 601 1_555 V O3G GTP . D GTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc22 U MG MG . D MG 601 1_555 V O2B GTP . D GTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 PG O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 7DBB _atom_sites.fract_transf_matrix[1][1] 0.009524 _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] 0.006346 _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] 0.005506 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 7 CA A 1 504 505 CA CA . K 8 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 7 CA B 1 503 503 CA CA . N 9 MES B 1 504 504 MES MES . O 9 MES B 1 505 505 MES MES . P 6 MG B 1 506 506 MG MG . Q 10 H1F B 1 507 601 H1F SSE . R 5 GTP C 1 501 501 GTP GTP . S 6 MG C 1 502 502 MG MG . T 7 CA C 1 503 503 CA CA . U 6 MG D 1 601 601 MG MG . V 5 GTP D 1 602 701 GTP GTP . W 11 ACP F 1 401 703 ACP ACP . # 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 PG ACP . . . W 11 8.426 49.281 93.941 1 138.06 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . W 11 6.911 49.279 93.827 1 97.28 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . W 11 9.049 50.38 93.093 1 93.45 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . W 11 9.025 47.976 93.454 1 122.78 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . W 11 10.757 49.626 95.792 1 125.32 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . W 11 11.308 50.694 94.864 1 121.09 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . W 11 11.302 48.285 95.36 1 107.31 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . W 11 8.898 49.511 95.724 1 106.7 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . W 11 10.367 50.93 98.431 1 113.54 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . W 11 8.974 51.277 97.95 1 97.3 -1 O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . W 11 11.142 52.192 98.706 1 116.34 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . W 11 11.19 49.978 97.351 1 115.18 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . W 11 10.222 50.082 99.834 1 110.84 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . W 11 9.487 48.886 99.829 1 109.33 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . W 11 8.801 48.719 101.211 1 93.18 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . W 11 9.552 49.252 102.135 1 88.77 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . W 11 7.511 49.552 101.26 1 86.47 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . W 11 6.468 48.815 100.807 1 89.72 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . W 11 7.359 49.857 102.759 1 86.14 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . W 11 6.609 48.737 103.392 1 91.59 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . W 11 8.567 49.877 103.252 1 81.72 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . W 11 9.003 51.209 103.581 1 82.24 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . W 11 9.729 52.027 102.821 1 83.32 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . W 11 9.917 53.159 103.506 1 84.14 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . W 11 9.313 53.04 104.693 1 73.87 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . W 11 9.204 53.904 105.763 1 85.3 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . W 11 9.714 55.253 105.979 1 73.9 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . W 11 8.535 53.52 106.836 1 91.03 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . W 11 7.957 52.295 106.879 1 88.35 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . W 11 8.065 51.454 105.824 1 79.19 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . W 11 8.748 51.833 104.737 1 69.89 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #