data_5SVP # _model_server_result.job_id 6UnmIHJ4gTOtiIk9n5fGWg _model_server_result.datetime_utc '2024-11-23 09:12:03' _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 5svp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 5SVP # _exptl.entry_id 5SVP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 5SVP _cell.length_a 172.93 _cell.length_b 172.93 _cell.length_c 172.93 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SVP _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 3' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,C,D,E,F,G,H,I 1 1,3,5 B,J,K,L,M,N,O 2 1,2,4 # 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' 5_564 z,x+1,y-1 0 0 1 1 0 0 0 1 0 0 172.93 -172.93 3 'crystal symmetry operation' 7_564 -z+1/2,-x+1,y-1/2 0 0 -1 -1 0 0 0 1 0 86.465 172.93 -86.465 4 'crystal symmetry operation' 9_465 y-1,z+1,x 0 1 0 0 0 1 1 0 0 -172.93 172.93 0 5 'crystal symmetry operation' 10_655 -y+1,z+1/2,-x+1/2 0 -1 0 0 0 1 -1 0 0 172.93 86.465 86.465 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id J _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 disulf ? disulf1 A SG CYS 106 A CYS 107 1_555 A SG CYS 152 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 121 A CYS 122 1_555 A SG CYS 146 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 202 A CYS 203 1_555 A SG CYS 212 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 246 A CYS 247 1_555 A SG CYS 255 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 106 B CYS 107 1_555 B SG CYS 152 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 B SG CYS 115 B CYS 116 1_555 B SG CYS 136 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 B SG CYS 121 B CYS 122 1_555 B SG CYS 146 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf9 B SG CYS 202 B CYS 203 1_555 B SG CYS 212 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf10 B SG CYS 246 B CYS 247 1_555 B SG CYS 255 B CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A ND2 ASN 169 A ASN 170 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 A ND2 ASN 193 A ASN 194 1_555 D C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 A ND2 ASN 289 A ASN 290 1_555 E C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale4 B ND2 ASN 169 B ASN 170 1_555 K C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 B ND2 ASN 193 B ASN 194 1_555 L C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.509 ? covale ? covale6 B ND2 ASN 289 B ASN 290 1_555 M C1 NAG . B NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? metalc ? metalc1 F OAI 6AT . A 6AT 404 1_555 G NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 123 n n PG O2G ATP sing 124 n n PG O3G ATP sing 125 n n PG O3B ATP sing 126 n n O2G HOG2 ATP sing 127 n n O3G HOG3 ATP sing 128 n n PB O1B ATP doub 129 n n PB O2B ATP sing 130 n n PB O3B ATP sing 131 n n PB O3A ATP sing 132 n n O2B HOB2 ATP sing 133 n n PA O1A ATP doub 134 n n PA O2A ATP sing 135 n n PA O3A ATP sing 136 n n PA O5' ATP sing 137 n n O2A HOA2 ATP sing 138 n n O5' C5' ATP sing 139 n n C5' C4' ATP sing 140 n n C5' "H5'1" ATP sing 141 n n C5' "H5'2" ATP sing 142 n n C4' O4' ATP sing 143 n n C4' C3' ATP sing 144 n n C4' H4' ATP sing 145 n n O4' C1' ATP sing 146 n n C3' O3' ATP sing 147 n n C3' C2' ATP sing 148 n n C3' H3' ATP sing 149 n n O3' HO3' ATP sing 150 n n C2' O2' ATP sing 151 n n C2' C1' ATP sing 152 n n C2' H2' ATP sing 153 n n O2' HO2' ATP sing 154 n n C1' N9 ATP sing 155 n n C1' H1' ATP sing 156 n n N9 C8 ATP sing 157 n y N9 C4 ATP sing 158 n y C8 N7 ATP doub 159 n y C8 H8 ATP sing 160 n n N7 C5 ATP sing 161 n y C5 C6 ATP sing 162 n y C5 C4 ATP doub 163 n y C6 N6 ATP sing 164 n n C6 N1 ATP doub 165 n y N6 HN61 ATP sing 166 n n N6 HN62 ATP sing 167 n n N1 C2 ATP sing 168 n y C2 N3 ATP doub 169 n y C2 H2 ATP sing 170 n n N3 C4 ATP sing 171 n y # _atom_sites.entry_id 5SVP _atom_sites.fract_transf_matrix[1][1] 0.005783 _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] 0.005783 _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] 0.005783 _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 C 2 NAG A 1 401 500 NAG NAG . D 2 NAG A 1 402 501 NAG NAG . E 2 NAG A 1 403 502 NAG NAG . F 3 6AT A 1 404 1 6AT LIG . G 4 NA A 1 405 4 NA NA . H 5 TRS A 1 406 1 TRS TRS . I 6 EDO A 1 407 1 EDO EDO . J 7 ATP B 1 401 402 ATP ATP . K 2 NAG B 1 402 500 NAG NAG . L 2 NAG B 1 403 501 NAG NAG . M 2 NAG B 1 404 502 NAG NAG . N 4 NA B 1 405 3 NA NA . O 6 EDO B 1 406 2 EDO EDO . # 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 ATP . . . J 7 7.935 167.357 24.087 1 81.85 ? PG ATP 401 B 1 HETATM 2 O O1G ATP . . . J 7 8.457 166.283 23.16 1 90.09 ? O1G ATP 401 B 1 HETATM 3 O O2G ATP . . . J 7 7.014 166.851 25.168 1 101.46 ? O2G ATP 401 B 1 HETATM 4 O O3G ATP . . . J 7 7.427 168.588 23.381 1 65.05 ? O3G ATP 401 B 1 HETATM 5 P PB ATP . . . J 7 10.699 167.294 24.577 1 62.47 ? PB ATP 401 B 1 HETATM 6 O O1B ATP . . . J 7 11.116 167.684 23.177 1 70.25 ? O1B ATP 401 B 1 HETATM 7 O O2B ATP . . . J 7 10.699 165.837 24.983 1 75.93 ? O2B ATP 401 B 1 HETATM 8 O O3B ATP . . . J 7 9.228 167.875 24.894 1 62.82 ? O3B ATP 401 B 1 HETATM 9 P PA ATP . . . J 7 11.985 169.653 25.53 1 89.31 ? PA ATP 401 B 1 HETATM 10 O O1A ATP . . . J 7 11.292 170.251 24.332 1 71.68 ? O1A ATP 401 B 1 HETATM 11 O O2A ATP . . . J 7 13.481 169.765 25.7 1 68.22 ? O2A ATP 401 B 1 HETATM 12 O O3A ATP . . . J 7 11.601 168.094 25.648 1 75.65 ? O3A ATP 401 B 1 HETATM 13 O O5' ATP . . . J 7 11.253 170.175 26.859 1 64.97 ? O5' ATP 401 B 1 HETATM 14 C C5' ATP . . . J 7 11.695 169.68 28.12 1 71.09 ? C5' ATP 401 B 1 HETATM 15 C C4' ATP . . . J 7 10.488 169.257 28.951 1 68.13 ? C4' ATP 401 B 1 HETATM 16 O O4' ATP . . . J 7 9.646 170.385 29.187 1 53.27 ? O4' ATP 401 B 1 HETATM 17 C C3' ATP . . . J 7 9.632 168.194 28.266 1 77.98 ? C3' ATP 401 B 1 HETATM 18 O O3' ATP . . . J 7 9.398 167.112 29.175 1 99.17 ? O3' ATP 401 B 1 HETATM 19 C C2' ATP . . . J 7 8.337 168.886 27.898 1 73.93 ? C2' ATP 401 B 1 HETATM 20 O O2' ATP . . . J 7 7.199 168.037 28.067 1 82.98 ? O2' ATP 401 B 1 HETATM 21 C C1' ATP . . . J 7 8.293 170.067 28.85 1 72.67 ? C1' ATP 401 B 1 HETATM 22 N N9 ATP . . . J 7 7.656 171.264 28.26 1 63.72 ? N9 ATP 401 B 1 HETATM 23 C C8 ATP . . . J 7 8.153 172.004 27.253 1 72.6 ? C8 ATP 401 B 1 HETATM 24 N N7 ATP . . . J 7 7.322 173.038 26.969 1 74.2 ? N7 ATP 401 B 1 HETATM 25 C C5 ATP . . . J 7 6.279 172.964 27.812 1 65.62 ? C5 ATP 401 B 1 HETATM 26 C C6 ATP . . . J 7 5.048 173.744 28.052 1 66.62 ? C6 ATP 401 B 1 HETATM 27 N N6 ATP . . . J 7 4.792 174.83 27.294 1 72.45 ? N6 ATP 401 B 1 HETATM 28 N N1 ATP . . . J 7 4.211 173.335 29.033 1 64.25 ? N1 ATP 401 B 1 HETATM 29 C C2 ATP . . . J 7 4.478 172.247 29.784 1 62.07 ? C2 ATP 401 B 1 HETATM 30 N N3 ATP . . . J 7 5.583 171.497 29.613 1 71.42 ? N3 ATP 401 B 1 HETATM 31 C C4 ATP . . . J 7 6.502 171.794 28.663 1 58.85 ? C4 ATP 401 B 1 HETATM 32 H "H5'1" ATP . . . J 7 12.358 168.826 27.97 1 85.3 ? "H5'1" ATP 401 B 1 HETATM 33 H "H5'2" ATP . . . J 7 12.253 170.457 28.647 1 85.3 ? "H5'2" ATP 401 B 1 HETATM 34 H H4' ATP . . . J 7 10.846 168.855 29.909 1 81.76 ? H4' ATP 401 B 1 HETATM 35 H H3' ATP . . . J 7 10.137 167.841 27.356 1 93.57 ? H3' ATP 401 B 1 HETATM 36 H HO3' ATP . . . J 7 8.856 166.438 28.742 1 119.01 ? HO3' ATP 401 B 1 HETATM 37 H H2' ATP . . . J 7 8.399 169.252 26.863 1 88.72 ? H2' ATP 401 B 1 HETATM 38 H HO2' ATP . . . J 7 7.281 167.268 27.486 1 99.58 ? HO2' ATP 401 B 1 HETATM 39 H H1' ATP . . . J 7 7.748 169.765 29.755 1 87.2 ? H1' ATP 401 B 1 HETATM 40 H H8 ATP . . . J 7 9.083 171.799 26.737 1 87.12 ? H8 ATP 401 B 1 HETATM 41 H HN61 ATP . . . J 7 3.952 175.368 27.45 1 86.94 ? HN61 ATP 401 B 1 HETATM 42 H HN62 ATP . . . J 7 5.44 175.104 26.569 1 86.94 ? HN62 ATP 401 B 1 HETATM 43 H H2 ATP . . . J 7 3.773 171.964 30.556 1 74.48 ? H2 ATP 401 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #