data_5VKF # _model_server_result.job_id IV8OGVA72_2lUN9kXhVFrw _model_server_result.datetime_utc '2024-10-10 02:29:25' _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 5vkf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":103}' # _entry.id 5VKF # _exptl.entry_id 5VKF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 128.171 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NAPHTHALENE _entity.pdbx_number_of_molecules 2 _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 5VKF _cell.length_a 110.359 _cell.length_b 110.359 _cell.length_c 70.827 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VKF _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_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 _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 # 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 I N N # _chem_comp.formula 'C10 H8' _chem_comp.formula_weight 128.171 _chem_comp.id NPY _chem_comp.mon_nstd_flag . _chem_comp.name NAPHTHALENE _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 C1 C2 NPY doub 184 n y C1 C8A NPY sing 185 n y C1 H11 NPY sing 186 n n C2 C3 NPY sing 187 n y C2 H2 NPY sing 188 n n C3 C4 NPY doub 189 n y C3 H3 NPY sing 190 n n C4 C4A NPY sing 191 n y C4 H4 NPY sing 192 n n C4A C5 NPY sing 193 n y C4A C8A NPY doub 194 n y C5 C6 NPY doub 195 n y C5 H5 NPY sing 196 n n C6 C7 NPY sing 197 n y C6 H6 NPY sing 198 n n C7 C8 NPY doub 199 n y C7 H7 NPY sing 200 n n C8 C8A NPY sing 201 n y C8 H8 NPY sing 202 n n # _atom_sites.entry_id 5VKF _atom_sites.fract_transf_matrix[1][1] 0.009061 _atom_sites.fract_transf_matrix[1][2] 0.005232 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010463 _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] 0.014119 _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 E 2 SO4 B 1 101 1 SO4 SO4 . F 2 SO4 B 1 102 2 SO4 SO4 . G 3 NPY B 1 103 1 NPY NPY . H 2 SO4 D 1 101 3 SO4 SO4 . I 3 NPY D 1 102 1 NPY NPY . J 4 HOH A 1 101 35 HOH HOH . J 4 HOH A 2 102 90 HOH HOH . J 4 HOH A 3 103 16 HOH HOH . J 4 HOH A 4 104 41 HOH HOH . J 4 HOH A 5 105 8 HOH HOH . J 4 HOH A 6 106 98 HOH HOH . J 4 HOH A 7 107 104 HOH HOH . J 4 HOH A 8 108 91 HOH HOH . J 4 HOH A 9 109 112 HOH HOH . J 4 HOH A 10 110 55 HOH HOH . J 4 HOH A 11 111 86 HOH HOH . J 4 HOH A 12 112 19 HOH HOH . J 4 HOH A 13 113 110 HOH HOH . J 4 HOH A 14 114 70 HOH HOH . J 4 HOH A 15 115 82 HOH HOH . J 4 HOH A 16 116 53 HOH HOH . J 4 HOH A 17 117 94 HOH HOH . J 4 HOH A 18 118 44 HOH HOH . J 4 HOH A 19 119 116 HOH HOH . J 4 HOH A 20 120 24 HOH HOH . J 4 HOH A 21 121 81 HOH HOH . J 4 HOH A 22 122 21 HOH HOH . J 4 HOH A 23 123 125 HOH HOH . J 4 HOH A 24 124 12 HOH HOH . J 4 HOH A 25 125 95 HOH HOH . J 4 HOH A 26 126 31 HOH HOH . J 4 HOH A 27 127 124 HOH HOH . J 4 HOH A 28 128 108 HOH HOH . J 4 HOH A 29 129 106 HOH HOH . J 4 HOH A 30 130 51 HOH HOH . K 4 HOH B 1 201 43 HOH HOH . K 4 HOH B 2 202 38 HOH HOH . K 4 HOH B 3 203 129 HOH HOH . K 4 HOH B 4 204 58 HOH HOH . K 4 HOH B 5 205 85 HOH HOH . K 4 HOH B 6 206 128 HOH HOH . K 4 HOH B 7 207 65 HOH HOH . K 4 HOH B 8 208 22 HOH HOH . K 4 HOH B 9 209 59 HOH HOH . K 4 HOH B 10 210 4 HOH HOH . K 4 HOH B 11 211 7 HOH HOH . K 4 HOH B 12 212 52 HOH HOH . K 4 HOH B 13 213 97 HOH HOH . K 4 HOH B 14 214 9 HOH HOH . K 4 HOH B 15 215 13 HOH HOH . K 4 HOH B 16 216 1 HOH HOH . K 4 HOH B 17 217 54 HOH HOH . K 4 HOH B 18 218 102 HOH HOH . K 4 HOH B 19 219 111 HOH HOH . K 4 HOH B 20 220 105 HOH HOH . K 4 HOH B 21 221 109 HOH HOH . K 4 HOH B 22 222 17 HOH HOH . K 4 HOH B 23 223 127 HOH HOH . K 4 HOH B 24 224 18 HOH HOH . K 4 HOH B 25 225 101 HOH HOH . K 4 HOH B 26 226 76 HOH HOH . K 4 HOH B 27 227 123 HOH HOH . K 4 HOH B 28 228 34 HOH HOH . K 4 HOH B 29 229 88 HOH HOH . K 4 HOH B 30 230 61 HOH HOH . K 4 HOH B 31 231 92 HOH HOH . K 4 HOH B 32 232 62 HOH HOH . K 4 HOH B 33 233 126 HOH HOH . K 4 HOH B 34 234 117 HOH HOH . K 4 HOH B 35 235 56 HOH HOH . K 4 HOH B 36 236 121 HOH HOH . K 4 HOH B 37 237 131 HOH HOH . L 4 HOH C 1 101 10 HOH HOH . L 4 HOH C 2 102 25 HOH HOH . L 4 HOH C 3 103 26 HOH HOH . L 4 HOH C 4 104 119 HOH HOH . L 4 HOH C 5 105 83 HOH HOH . L 4 HOH C 6 106 11 HOH HOH . L 4 HOH C 7 107 23 HOH HOH . L 4 HOH C 8 108 39 HOH HOH . L 4 HOH C 9 109 72 HOH HOH . L 4 HOH C 10 110 20 HOH HOH . L 4 HOH C 11 111 120 HOH HOH . L 4 HOH C 12 112 96 HOH HOH . L 4 HOH C 13 113 66 HOH HOH . L 4 HOH C 14 114 78 HOH HOH . L 4 HOH C 15 115 100 HOH HOH . L 4 HOH C 16 116 71 HOH HOH . L 4 HOH C 17 117 36 HOH HOH . L 4 HOH C 18 118 74 HOH HOH . L 4 HOH C 19 119 73 HOH HOH . L 4 HOH C 20 120 122 HOH HOH . L 4 HOH C 21 121 67 HOH HOH . L 4 HOH C 22 122 30 HOH HOH . L 4 HOH C 23 123 113 HOH HOH . L 4 HOH C 24 124 45 HOH HOH . M 4 HOH D 1 201 99 HOH HOH . M 4 HOH D 2 202 80 HOH HOH . M 4 HOH D 3 203 37 HOH HOH . M 4 HOH D 4 204 40 HOH HOH . M 4 HOH D 5 205 6 HOH HOH . M 4 HOH D 6 206 15 HOH HOH . M 4 HOH D 7 207 93 HOH HOH . M 4 HOH D 8 208 89 HOH HOH . M 4 HOH D 9 209 57 HOH HOH . M 4 HOH D 10 210 47 HOH HOH . M 4 HOH D 11 211 32 HOH HOH . M 4 HOH D 12 212 3 HOH HOH . M 4 HOH D 13 213 33 HOH HOH . M 4 HOH D 14 214 46 HOH HOH . M 4 HOH D 15 215 79 HOH HOH . M 4 HOH D 16 216 42 HOH HOH . M 4 HOH D 17 217 84 HOH HOH . M 4 HOH D 18 218 50 HOH HOH . M 4 HOH D 19 219 29 HOH HOH . M 4 HOH D 20 220 103 HOH HOH . M 4 HOH D 21 221 115 HOH HOH . M 4 HOH D 22 222 118 HOH HOH . M 4 HOH D 23 223 14 HOH HOH . M 4 HOH D 24 224 27 HOH HOH . M 4 HOH D 25 225 107 HOH HOH . M 4 HOH D 26 226 68 HOH HOH . M 4 HOH D 27 227 48 HOH HOH . M 4 HOH D 28 228 87 HOH HOH . M 4 HOH D 29 229 114 HOH HOH . M 4 HOH D 30 230 28 HOH HOH . M 4 HOH D 31 231 49 HOH HOH . M 4 HOH D 32 232 69 HOH HOH . M 4 HOH D 33 233 75 HOH HOH . M 4 HOH D 34 234 63 HOH HOH . M 4 HOH D 35 235 130 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 C C1 NPY . A . G 3 47.72 31.88 14.264 0.75 76.97 ? C1 NPY 103 B 1 HETATM 2 C C1 NPY . B . G 3 49.908 31.596 15.268 0.25 76.44 ? C1 NPY 103 B 1 HETATM 3 C C2 NPY . A . G 3 47.99 31.876 15.629 0.75 76.84 ? C2 NPY 103 B 1 HETATM 4 C C2 NPY . B . G 3 51.278 31.794 15.127 0.25 76.74 ? C2 NPY 103 B 1 HETATM 5 C C3 NPY . A . G 3 49.299 31.818 16.104 0.75 76.75 ? C3 NPY 103 B 1 HETATM 6 C C3 NPY . B . G 3 51.853 32.014 13.877 0.25 76.74 ? C3 NPY 103 B 1 HETATM 7 C C4 NPY . A . G 3 50.382 31.761 15.232 0.75 76.77 ? C4 NPY 103 B 1 HETATM 8 C C4 NPY . B . G 3 51.075 32.043 12.723 0.25 76.95 ? C4 NPY 103 B 1 HETATM 9 C C4A NPY . A . G 3 50.16 31.763 13.863 0.75 78.17 ? C4A NPY 103 B 1 HETATM 10 C C4A NPY . B . G 3 49.705 31.849 12.815 0.25 75.75 ? C4A NPY 103 B 1 HETATM 11 C C5 NPY . A . G 3 51.208 31.708 12.956 0.75 77.19 ? C5 NPY 103 B 1 HETATM 12 C C5 NPY . B . G 3 48.892 31.87 11.692 0.25 76.86 ? C5 NPY 103 B 1 HETATM 13 C C6 NPY . A . G 3 50.938 31.712 11.591 0.75 77.1 ? C6 NPY 103 B 1 HETATM 14 C C6 NPY . B . G 3 47.522 31.671 11.83 0.25 76.91 ? C6 NPY 103 B 1 HETATM 15 C C7 NPY . A . G 3 49.63 31.771 11.115 0.75 76.96 ? C7 NPY 103 B 1 HETATM 16 C C7 NPY . B . G 3 46.947 31.451 13.081 0.25 76.9 ? C7 NPY 103 B 1 HETATM 17 C C8 NPY . A . G 3 48.547 31.827 11.988 0.75 77.39 ? C8 NPY 103 B 1 HETATM 18 C C8 NPY . B . G 3 47.723 31.423 14.235 0.25 76.96 ? C8 NPY 103 B 1 HETATM 19 C C8A NPY . A . G 3 48.768 31.825 13.357 0.75 76.99 ? C8A NPY 103 B 1 HETATM 20 C C8A NPY . B . G 3 49.094 31.616 14.145 0.25 77.87 ? C8A NPY 103 B 1 HETATM 21 H H11 NPY . A . G 3 46.697 31.927 13.912 0.75 92.41 ? H11 NPY 103 B 1 HETATM 22 H H11 NPY . B . G 3 49.48 31.426 16.248 0.25 91.77 ? H11 NPY 103 B 1 HETATM 23 H H2 NPY . A . G 3 47.169 31.919 16.334 0.75 92.25 ? H2 NPY 103 B 1 HETATM 24 H H2 NPY . B . G 3 51.91 31.778 16.007 0.25 92.13 ? H2 NPY 103 B 1 HETATM 25 H H3 NPY . A . G 3 49.477 31.816 17.172 0.75 92.14 ? H3 NPY 103 B 1 HETATM 26 H H3 NPY . B . G 3 52.923 32.166 13.801 0.25 92.14 ? H3 NPY 103 B 1 HETATM 27 H H4 NPY . A . G 3 51.392 31.716 15.62 0.75 92.16 ? H4 NPY 103 B 1 HETATM 28 H H4 NPY . B . G 3 51.537 32.215 11.759 0.25 92.38 ? H4 NPY 103 B 1 HETATM 29 H H5 NPY . A . G 3 52.231 31.661 13.308 0.75 92.67 ? H5 NPY 103 B 1 HETATM 30 H H5 NPY . B . G 3 49.321 32.039 10.712 0.25 92.27 ? H5 NPY 103 B 1 HETATM 31 H H6 NPY . A . G 3 51.759 31.669 10.886 0.75 92.56 ? H6 NPY 103 B 1 HETATM 32 H H6 NPY . B . G 3 46.89 31.688 10.95 0.25 92.34 ? H6 NPY 103 B 1 HETATM 33 H H7 NPY . A . G 3 49.452 31.772 10.047 0.75 92.4 ? H7 NPY 103 B 1 HETATM 34 H H7 NPY . B . G 3 45.877 31.3 13.155 0.25 92.33 ? H7 NPY 103 B 1 HETATM 35 H H8 NPY . A . G 3 47.537 31.872 11.6 0.75 92.91 ? H8 NPY 103 B 1 HETATM 36 H H8 NPY . B . G 3 47.26 31.251 15.199 0.25 92.39 ? H8 NPY 103 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 36 #