data_4RVZ # _model_server_result.job_id v7XFuqqpbEwjp882dfql7A _model_server_result.datetime_utc '2024-12-28 01:27:22' _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 4rvz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 4RVZ # _exptl.entry_id 4RVZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _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 4RVZ _cell.length_a 69.623 _cell.length_b 69.623 _cell.length_c 211.269 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RVZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 3 _struct_asym.id C _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 CYS 17 Z CYS 17 1_555 A N TPO 18 Z TPO 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C TPO 18 Z TPO 18 1_555 A N THR 19 Z THR 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OD2 ASP 8 Z ASP 8 1_555 E MG MG . Z MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc2 A OD1 ASP 9 Z ASP 9 1_555 D MG MG . Z MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc3 A O ASP 11 Z ASP 11 1_555 D MG MG . Z MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc4 A O2P TPO 18 Z TPO 18 1_555 E MG MG . Z MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc5 A SG CYS 352 Z CYS 352 1_555 B ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc6 A SG CYS 355 Z CYS 355 1_555 B ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc7 A SG CYS 370 Z CYS 370 1_555 B ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc8 A SG CYS 373 Z CYS 373 1_555 B ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? metalc ? metalc9 C O1A ACP . Z ACP 502 1_555 D MG MG . Z MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc10 C O1B ACP . Z ACP 502 1_555 E MG MG . Z MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc11 C O2A ACP . Z ACP 502 1_555 E MG MG . Z MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? # _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 4RVZ _atom_sites.fract_transf_matrix[1][1] 0.014363 _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] 0.014363 _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] 0.004733 _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 ZN Z 1 501 1 ZN ZN . C 3 ACP Z 1 502 1 ACP ACP . D 4 MG Z 1 503 1 MG MG . E 4 MG Z 1 504 2 MG MG . F 5 ZNN Z 1 505 1 ZNN NNN . # 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 . . . C 3 19.576 7.729 37.732 1 259.47 ? PG ACP 502 Z 1 HETATM 2 O O1G ACP . . . C 3 20.239 8.192 36.349 1 69.32 ? O1G ACP 502 Z 1 HETATM 3 O O2G ACP . . . C 3 21.008 8.408 38.263 1 176.16 ? O2G ACP 502 Z 1 HETATM 4 O O3G ACP . . . C 3 18.796 9.278 37.563 1 96.53 ? O3G ACP 502 Z 1 HETATM 5 P PB ACP . . . C 3 17.636 4.249 38.178 1 154.2 ? PB ACP 502 Z 1 HETATM 6 O O1B ACP . . . C 3 16.89 4.748 38.888 1 150.69 ? O1B ACP 502 Z 1 HETATM 7 O O2B ACP . . . C 3 18.482 3.536 39.01 1 157.57 ? O2B ACP 502 Z 1 HETATM 8 C C3B ACP . . . C 3 18.697 5.913 38.015 1 39.84 ? C3B ACP 502 Z 1 HETATM 9 P PA ACP . . . C 3 18.752 2.941 36.053 1 97.27 ? PA ACP 502 Z 1 HETATM 10 O O1A ACP . . . C 3 19.48 3.377 34.983 1 107.15 ? O1A ACP 502 Z 1 HETATM 11 O O2A ACP . . . C 3 17.342 3.036 35.788 1 97.46 ? O2A ACP 502 Z 1 HETATM 12 O O3A ACP . . . C 3 19.006 3.883 37.274 1 89.08 ? O3A ACP 502 Z 1 HETATM 13 O O5' ACP . . . C 3 19.041 1.231 36.364 1 71.69 ? O5' ACP 502 Z 1 HETATM 14 C C5' ACP . . . C 3 18.075 0.592 37.281 1 75.52 ? C5' ACP 502 Z 1 HETATM 15 C C4' ACP . . . C 3 17.141 -0.489 36.808 1 73.26 ? C4' ACP 502 Z 1 HETATM 16 O O4' ACP . . . C 3 17.024 -1.456 37.787 1 75.34 ? O4' ACP 502 Z 1 HETATM 17 C C3' ACP . . . C 3 15.791 0.086 36.662 1 74.61 ? C3' ACP 502 Z 1 HETATM 18 O O3' ACP . . . C 3 15.144 -0.581 35.594 1 86.97 ? O3' ACP 502 Z 1 HETATM 19 C C2' ACP . . . C 3 15.099 -0.214 37.821 1 67.01 ? C2' ACP 502 Z 1 HETATM 20 O O2' ACP . . . C 3 13.709 -0.352 37.512 1 56.22 ? O2' ACP 502 Z 1 HETATM 21 C C1' ACP . . . C 3 15.619 -1.416 38.264 1 75.45 ? C1' ACP 502 Z 1 HETATM 22 N N9 ACP . . . C 3 15.435 -1.537 39.763 1 84.95 ? N9 ACP 502 Z 1 HETATM 23 C C8 ACP . . . C 3 15.314 -0.51 40.61 1 86.6 ? C8 ACP 502 Z 1 HETATM 24 N N7 ACP . . . C 3 15.163 -1.007 41.866 1 87.19 ? N7 ACP 502 Z 1 HETATM 25 C C5 ACP . . . C 3 15.189 -2.366 41.796 1 86.64 ? C5 ACP 502 Z 1 HETATM 26 C C6 ACP . . . C 3 15.081 -3.398 42.772 1 82.4 ? C6 ACP 502 Z 1 HETATM 27 N N6 ACP . . . C 3 14.909 -3.102 44.083 1 82.48 ? N6 ACP 502 Z 1 HETATM 28 N N1 ACP . . . C 3 15.153 -4.685 42.35 1 76.86 ? N1 ACP 502 Z 1 HETATM 29 C C2 ACP . . . C 3 15.319 -4.99 41.054 1 81.62 ? C2 ACP 502 Z 1 HETATM 30 N N3 ACP . . . C 3 15.424 -4.029 40.12 1 87.69 ? N3 ACP 502 Z 1 HETATM 31 C C4 ACP . . . C 3 15.363 -2.719 40.459 1 87.07 ? C4 ACP 502 Z 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 31 #