data_8ZB8 # _model_server_result.job_id HYLKT7QP8JuM-ev1wyJMuw _model_server_result.datetime_utc '2024-11-14 18:47:35' _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 8zb8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":401}' # _entry.id 8ZB8 # _exptl.entry_id 8ZB8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 12 _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 8ZB8 _cell.length_a 105.599 _cell.length_b 158.202 _cell.length_c 180.521 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ZB8 _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 _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 12 _struct_asym.id T _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.088 ? metalc ? metalc3 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc5 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc6 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc7 G O3G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc8 G O2B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc9 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc10 K O2A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc11 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc12 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc13 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc14 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc15 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc16 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc17 O O3G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc18 O O2B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? # _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 42 n n PG O2G ACP sing 43 n n PG O3G ACP sing 44 n n PG C3B ACP sing 45 n n O2G HOG2 ACP sing 46 n n O3G HOG3 ACP sing 47 n n PB O1B ACP doub 48 n n PB O2B ACP sing 49 n n PB C3B ACP sing 50 n n PB O3A ACP sing 51 n n O2B HOB2 ACP sing 52 n n C3B H3B1 ACP sing 53 n n C3B H3B2 ACP sing 54 n n PA O1A ACP doub 55 n n PA O2A ACP sing 56 n n PA O3A ACP sing 57 n n PA O5' ACP sing 58 n n O2A HOA2 ACP sing 59 n n O5' C5' ACP sing 60 n n C5' C4' ACP sing 61 n n C5' "H5'1" ACP sing 62 n n C5' "H5'2" ACP sing 63 n n C4' O4' ACP sing 64 n n C4' C3' ACP sing 65 n n C4' H4' ACP sing 66 n n O4' C1' ACP sing 67 n n C3' O3' ACP sing 68 n n C3' C2' ACP sing 69 n n C3' H3' ACP sing 70 n n O3' HO3' ACP sing 71 n n C2' O2' ACP sing 72 n n C2' C1' ACP sing 73 n n C2' H2' ACP sing 74 n n O2' HO2' ACP sing 75 n n C1' N9 ACP sing 76 n n C1' H1' ACP sing 77 n n N9 C8 ACP sing 78 n y N9 C4 ACP sing 79 n y C8 N7 ACP doub 80 n y C8 H8 ACP sing 81 n n N7 C5 ACP sing 82 n y C5 C6 ACP sing 83 n y C5 C4 ACP doub 84 n y C6 N6 ACP sing 85 n n C6 N1 ACP doub 86 n y N6 HN61 ACP sing 87 n n N6 HN62 ACP sing 88 n n N1 C2 ACP sing 89 n y C2 N3 ACP doub 90 n y C2 H2 ACP sing 91 n n N3 C4 ACP sing 92 n y # _atom_sites.entry_id 8ZB8 _atom_sites.fract_transf_matrix[1][1] 0.00947 _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] 0.006321 _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] 0.00554 _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 8 GOL A 1 504 504 GOL GOL . K 9 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 10 MES B 1 503 503 MES MES . N 11 A1D8I B 1 504 601 A1D8I KKK . O 5 GTP C 1 501 501 GTP GTP . P 6 MG C 1 502 502 MG MG . Q 7 CA C 1 503 503 CA CA . R 9 GDP D 1 501 501 GDP GDP . S 11 A1D8I D 1 502 601 A1D8I KKK . T 12 ACP F 1 401 401 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 . . . T 12 9.073 -51.498 -94.072 1 124.2 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . T 12 10.522 -51.445 -93.683 1 105.16 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . T 12 8.547 -52.956 -94.162 1 100.38 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . T 12 8.168 -50.706 -93.094 1 109.13 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . T 12 10.283 -49.923 -96.441 1 117.11 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . T 12 10.282 -48.502 -95.925 1 110.93 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . T 12 11.631 -50.634 -96.074 1 108.11 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . T 12 8.815 -50.759 -95.694 1 104.9 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . T 12 10.214 -51.378 -98.886 1 105.34 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . T 12 11.558 -51.996 -98.948 1 103.65 -1 O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . T 12 9.042 -52.225 -98.371 1 99.78 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . T 12 10.195 -49.916 -98.081 1 112.41 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . T 12 9.837 -50.965 -100.362 1 97.67 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . T 12 9.97 -49.597 -100.807 1 97.32 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . T 12 8.797 -49.176 -101.657 1 92.7 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . T 12 9.115 -49.418 -103.042 1 87.84 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . T 12 7.48 -49.896 -101.377 1 94.41 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . T 12 6.663 -49.1 -100.523 1 90.71 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . T 12 6.857 -50.066 -102.77 1 87.62 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . T 12 6.067 -48.946 -103.152 1 92.79 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . T 12 8.079 -50.132 -103.682 1 85.75 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . T 12 8.579 -51.461 -103.989 1 88.26 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . T 12 9.445 -52.201 -103.229 1 92.8 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . T 12 9.767 -53.356 -103.757 1 95.44 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . T 12 9.079 -53.37 -104.962 1 93.01 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . T 12 8.995 -54.322 -105.997 1 92.11 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . T 12 9.642 -55.492 -105.983 1 90.94 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . T 12 8.218 -54.026 -107.062 1 88.05 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . T 12 7.566 -52.859 -107.076 1 89.24 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . T 12 7.565 -51.886 -106.16 1 92.59 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . T 12 8.349 -52.203 -105.123 1 92.67 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #