data_5VV9 # _model_server_result.job_id dof5kDuX3x1YtsuYJgMHWQ _model_server_result.datetime_utc '2024-11-04 20:37:11' _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 5vv9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 5VV9 # _exptl.entry_id 5VV9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 241.247 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5,6,7,8-TETRAHYDROBIOPTERIN _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 90 _cell.entry_id 5VV9 _cell.length_a 57.245 _cell.length_b 106.127 _cell.length_c 155.832 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VV9 _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 PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 D N N ? 3 H 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 covale ? covale1 A C VAL 344 A VAL 383 1_555 A N CAS 345 A CAS 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale2 A C CAS 345 A CAS 384 1_555 A N MET 346 A MET 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 B C VAL 344 B VAL 383 1_555 B N CAS 345 B CAS 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale4 B C CAS 345 B CAS 384 1_555 B N MET 346 B MET 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? metalc ? metalc1 A SG CYS 57 A CYS 96 1_555 K ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc2 A SG CYS 62 A CYS 101 1_555 K ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc3 A SG CYS 147 A CYS 186 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc4 B SG CYS 57 B CYS 96 1_555 K ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc5 B SG CYS 62 B CYS 101 1_555 K ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc6 B SG CYS 147 B CYS 186 1_555 G FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? # _chem_comp.formula 'C9 H15 N5 O3' _chem_comp.formula_weight 241.247 _chem_comp.id H4B _chem_comp.mon_nstd_flag . _chem_comp.name 5,6,7,8-TETRAHYDROBIOPTERIN _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 N1 C2 H4B doub 209 n y N1 C8A H4B sing 210 n y C2 N2 H4B sing 211 n n C2 N3 H4B sing 212 n y N2 HN21 H4B sing 213 n n N2 HN22 H4B sing 214 n n N3 C4 H4B sing 215 n y N3 HN3 H4B sing 216 n n C4 O4 H4B doub 217 n n C4 C4A H4B sing 218 n y C4A C8A H4B doub 219 n y C4A N5 H4B sing 220 n n C8A N8 H4B sing 221 n n N5 C6 H4B sing 222 n n N5 HN5 H4B sing 223 n n N8 C7 H4B sing 224 n n N8 HN8 H4B sing 225 n n C6 C7 H4B sing 226 n n C6 C9 H4B sing 227 n n C6 H6 H4B sing 228 n n C7 H71 H4B sing 229 n n C7 H72 H4B sing 230 n n C9 O9 H4B sing 231 n n C9 C10 H4B sing 232 n n C9 H9 H4B sing 233 n n O9 HO9 H4B sing 234 n n C10 C11 H4B sing 235 n n C10 O10 H4B sing 236 n n C10 H10 H4B sing 237 n n C11 H111 H4B sing 238 n n C11 H112 H4B sing 239 n n C11 H113 H4B sing 240 n n O10 HO0 H4B sing 241 n n # _atom_sites.entry_id 5VV9 _atom_sites.fract_transf_matrix[1][1] 0.017469 _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] 0.009423 _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] 0.006417 _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 HEM A 1 501 500 HEM HEM . D 3 H4B A 1 502 600 H4B BH4 . E 4 9OG A 1 503 800 9OG 2P7 . F 5 GOL A 1 504 880 GOL GOL . G 2 HEM B 1 501 500 HEM HEM . H 3 H4B B 1 502 600 H4B BH4 . I 4 9OG B 1 503 800 9OG 2P7 . J 5 GOL B 1 504 880 GOL GOL . K 6 ZN B 1 505 900 ZN ZN . # 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 N N1 H4B . . . D 3 8.224 12.13 42.762 1 85.81 ? N1 H4B 502 A 1 HETATM 2 C C2 H4B . . . D 3 8.232 12.412 41.438 1 88.13 ? C2 H4B 502 A 1 HETATM 3 N N2 H4B . . . D 3 7.38 11.757 40.618 1 75.33 ? N2 H4B 502 A 1 HETATM 4 N N3 H4B . . . D 3 9.082 13.339 40.931 1 91.24 ? N3 H4B 502 A 1 HETATM 5 C C4 H4B . . . D 3 9.936 14.002 41.742 1 90.25 ? C4 H4B 502 A 1 HETATM 6 O O4 H4B . . . D 3 10.729 14.855 41.287 1 93.32 ? O4 H4B 502 A 1 HETATM 7 C C4A H4B . . . D 3 9.941 13.71 43.088 1 83.37 ? C4A H4B 502 A 1 HETATM 8 C C8A H4B . . . D 3 9.074 12.77 43.597 1 80.82 ? C8A H4B 502 A 1 HETATM 9 N N5 H4B . . . D 3 10.778 14.343 43.917 1 81.45 ? N5 H4B 502 A 1 HETATM 10 N N8 H4B . . . D 3 9.068 12.492 44.924 1 74.95 ? N8 H4B 502 A 1 HETATM 11 C C6 H4B . . . D 3 11.14 13.67 45.141 1 71.04 ? C6 H4B 502 A 1 HETATM 12 C C7 H4B . . . D 3 9.904 13.193 45.881 1 66.09 ? C7 H4B 502 A 1 HETATM 13 C C9 H4B . . . D 3 11.945 14.608 46.018 1 74.07 ? C9 H4B 502 A 1 HETATM 14 O O9 H4B . . . D 3 11.157 15.727 46.422 1 82.07 ? O9 H4B 502 A 1 HETATM 15 C C10 H4B . . . D 3 12.374 13.83 47.238 1 75.53 ? C10 H4B 502 A 1 HETATM 16 C C11 H4B . . . D 3 13.416 14.612 48.027 1 75.7 ? C11 H4B 502 A 1 HETATM 17 O O10 H4B . . . D 3 12.893 12.572 46.776 1 77.85 ? O10 H4B 502 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 17 #