data_7SSJ # _model_server_result.job_id YUaRIe_FUrFfDBH9WDyTYg _model_server_result.datetime_utc '2024-10-20 01:34:02' _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 7ssj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 7SSJ # _exptl.entry_id 7SSJ _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 3 _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 120 _cell.entry_id 7SSJ _cell.length_a 94.691 _cell.length_b 94.691 _cell.length_c 240.85 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7SSJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,I,J,T,U 1 1,2 C,D,E,F,K,L,M,N,O,P,Q,R,S,V,W,X,Y 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 G N N ? 3 K N N ? 3 M N 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 OE2 GLU 143 A GLU 289 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc2 A OD1 ASN 147 A ASN 293 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc3 G O3G ACP . A ACP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc4 G O2B ACP . A ACP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc5 G O1A ACP . A ACP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc6 H MG MG . A MG 402 1_555 T O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc7 T O HOH . A HOH 501 1_555 I MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc8 B OD1 ASP 13 B ASP 9 1_555 I MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc9 B OD2 ASP 58 B ASP 54 1_555 I MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc10 B OD1 ASP 58 B ASP 54 1_555 J BE BEF . B BEF 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.616 ? metalc ? metalc11 B O GLU 60 B GLU 56 1_555 I MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc12 I MG MG . B MG 201 1_555 U O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc13 C OE2 GLU 143 C GLU 289 1_555 L MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc14 C OD1 ASN 147 C ASN 293 1_555 L MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc15 K O3G ACP . C ACP 401 1_555 L MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc16 K O2B ACP . C ACP 401 1_555 L MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc17 K O1A ACP . C ACP 401 1_555 L MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc18 L MG MG . C MG 402 1_555 V O HOH . C HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc19 V O HOH . C HOH 501 1_555 O MG MG . E MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc20 D OE2 GLU 143 D GLU 289 1_555 N MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc21 D OD1 ASN 147 D ASN 293 1_555 N MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc22 M O3G ACP . D ACP 401 1_555 N MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc23 M O2B ACP . D ACP 401 1_555 N MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc24 M O1A ACP . D ACP 401 1_555 N MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc25 N MG MG . D MG 402 1_555 W O HOH . D HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc26 W O HOH . D HOH 503 1_555 R MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc27 E OD1 ASP 13 E ASP 9 1_555 O MG MG . E MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc28 E OD2 ASP 58 E ASP 54 1_555 O MG MG . E MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc29 E OD1 ASP 58 E ASP 54 1_555 P BE BEF . E BEF 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.564 ? metalc ? metalc30 E O GLU 60 E GLU 56 1_555 O MG MG . E MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc31 O MG MG . E MG 201 1_555 X O HOH . E HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc32 F OD1 ASP 13 F ASP 9 1_555 R MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc33 F OD2 ASP 58 F ASP 54 1_555 R MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc34 F OD1 ASP 58 F ASP 54 1_555 S BE BEF . F BEF 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.498 ? metalc ? metalc35 F O GLU 60 F GLU 56 1_555 R MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc36 R MG MG . F MG 201 1_555 Y O HOH . F HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? # _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 7SSJ _atom_sites.fract_transf_matrix[1][1] 0.010561 _atom_sites.fract_transf_matrix[1][2] 0.006097 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012194 _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] 0.004152 _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 3 ACP A 1 401 400 ACP ACP . H 4 MG A 1 402 410 MG MG . I 4 MG B 1 201 201 MG MG . J 5 BEF B 1 202 301 BEF BEF . K 3 ACP C 1 401 400 ACP ACP . L 4 MG C 1 402 410 MG MG . M 3 ACP D 1 401 400 ACP ACP . N 4 MG D 1 402 410 MG MG . O 4 MG E 1 201 201 MG MG . P 5 BEF E 1 202 301 BEF BEF . Q 6 SO4 E 1 203 1 SO4 SO4 . R 4 MG F 1 201 201 MG MG . S 5 BEF F 1 202 301 BEF BEF . T 7 HOH A 1 501 5 HOH HOH . T 7 HOH A 2 502 16 HOH HOH . T 7 HOH A 3 503 1 HOH HOH . T 7 HOH A 4 504 12 HOH HOH . T 7 HOH A 5 505 20 HOH HOH . T 7 HOH A 6 506 18 HOH HOH . T 7 HOH A 7 507 17 HOH HOH . U 7 HOH B 1 301 11 HOH HOH . U 7 HOH B 2 302 15 HOH HOH . U 7 HOH B 3 303 4 HOH HOH . V 7 HOH C 1 501 7 HOH HOH . V 7 HOH C 2 502 2 HOH HOH . W 7 HOH D 1 501 13 HOH HOH . W 7 HOH D 2 502 3 HOH HOH . W 7 HOH D 3 503 9 HOH HOH . X 7 HOH E 1 301 10 HOH HOH . X 7 HOH E 2 302 14 HOH HOH . X 7 HOH E 3 303 19 HOH HOH . X 7 HOH E 4 304 6 HOH HOH . X 7 HOH E 5 305 21 HOH HOH . Y 7 HOH F 1 301 8 HOH HOH . Y 7 HOH F 2 302 22 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 PG ACP . . . G 3 -27.336 -25.829 24.4 1 96.5 ? PG ACP 401 A 1 HETATM 2 O O1G ACP . . . G 3 -27.745 -26.429 23.093 1 96.57 ? O1G ACP 401 A 1 HETATM 3 O O2G ACP . . . G 3 -27.413 -24.286 24.367 1 97.09 ? O2G ACP 401 A 1 HETATM 4 O O3G ACP . . . G 3 -25.895 -26.214 24.803 1 95.43 ? O3G ACP 401 A 1 HETATM 5 P PB ACP . . . G 3 -27.801 -27.54 26.936 1 96.86 ? PB ACP 401 A 1 HETATM 6 O O1B ACP . . . G 3 -28.758 -27.955 28.04 1 97.73 ? O1B ACP 401 A 1 HETATM 7 O O2B ACP . . . G 3 -26.53 -26.905 27.593 1 96.85 ? O2B ACP 401 A 1 HETATM 8 C C3B ACP . . . G 3 -28.422 -26.351 25.736 1 97.15 ? C3B ACP 401 A 1 HETATM 9 P PA ACP . . . G 3 -25.949 -29.689 26.194 1 92.55 ? PA ACP 401 A 1 HETATM 10 O O1A ACP . . . G 3 -24.762 -28.814 26.155 1 92.11 ? O1A ACP 401 A 1 HETATM 11 O O2A ACP . . . G 3 -25.932 -30.641 25.016 1 91.86 ? O2A ACP 401 A 1 HETATM 12 O O3A ACP . . . G 3 -27.274 -28.809 26.093 1 94.87 ? O3A ACP 401 A 1 HETATM 13 O O5' ACP . . . G 3 -26.069 -30.539 27.529 1 91.85 ? O5' ACP 401 A 1 HETATM 14 C C5' ACP . . . G 3 -27.194 -31.425 27.632 1 92.1 ? C5' ACP 401 A 1 HETATM 15 C C4' ACP . . . G 3 -27.473 -31.656 29.09 1 92.93 ? C4' ACP 401 A 1 HETATM 16 O O4' ACP . . . G 3 -26.367 -32.374 29.68 1 92.76 ? O4' ACP 401 A 1 HETATM 17 C C3' ACP . . . G 3 -27.611 -30.403 29.946 1 93.55 ? C3' ACP 401 A 1 HETATM 18 O O3' ACP . . . G 3 -28.907 -29.819 29.873 1 94.28 ? O3' ACP 401 A 1 HETATM 19 C C2' ACP . . . G 3 -27.302 -30.945 31.338 1 94.05 ? C2' ACP 401 A 1 HETATM 20 O O2' ACP . . . G 3 -28.443 -31.64 31.832 1 95.23 ? O2' ACP 401 A 1 HETATM 21 C C1' ACP . . . G 3 -26.183 -31.949 31.023 1 93.13 ? C1' ACP 401 A 1 HETATM 22 N N9 ACP . . . G 3 -24.827 -31.422 31.175 1 92.11 ? N9 ACP 401 A 1 HETATM 23 C C8 ACP . . . G 3 -23.939 -31.078 30.186 1 90.73 ? C8 ACP 401 A 1 HETATM 24 N N7 ACP . . . G 3 -22.766 -30.682 30.623 1 90.32 ? N7 ACP 401 A 1 HETATM 25 C C5 ACP . . . G 3 -22.882 -30.773 32.003 1 91.36 ? C5 ACP 401 A 1 HETATM 26 C C6 ACP . . . G 3 -21.967 -30.57 33.055 1 91.49 ? C6 ACP 401 A 1 HETATM 27 N N6 ACP . . . G 3 -20.726 -30.116 32.888 1 91.06 ? N6 ACP 401 A 1 HETATM 28 N N1 ACP . . . G 3 -22.382 -30.844 34.31 1 92.53 ? N1 ACP 401 A 1 HETATM 29 C C2 ACP . . . G 3 -23.635 -31.268 34.497 1 93.09 ? C2 ACP 401 A 1 HETATM 30 N N3 ACP . . . G 3 -24.596 -31.491 33.593 1 92.97 ? N3 ACP 401 A 1 HETATM 31 C C4 ACP . . . G 3 -24.159 -31.228 32.359 1 92.22 ? C4 ACP 401 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 48 _model_server_stats.query_time_ms 465 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #