data_5VVA # _model_server_result.job_id nbdi62qULlipuI_mrWQCXA _model_server_result.datetime_utc '2024-11-25 06:43:03' _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 5vva # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 5VVA # _exptl.entry_id 5VVA _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 5VVA _cell.length_a 57.27 _cell.length_b 105.95 _cell.length_c 155.41 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VVA _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,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 D N N ? 3 I 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C CAS 345 A CAS 384 1_555 A N MET 346 A MET 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 B C VAL 344 B VAL 383 1_555 B N CAS 345 B CAS 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 B C CAS 345 B CAS 384 1_555 B N MET 346 B MET 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 A SG CYS 57 A CYS 96 1_555 G ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc2 A SG CYS 62 A CYS 101 1_555 G ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc3 A SG CYS 147 A CYS 186 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc4 G ZN ZN . A ZN 505 1_555 B SG CYS 57 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc5 G ZN ZN . A ZN 505 1_555 B SG CYS 62 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc6 B SG CYS 147 B CYS 186 1_555 H FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? # _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 212 n y N1 C8A H4B sing 213 n y C2 N2 H4B sing 214 n n C2 N3 H4B sing 215 n y N2 HN21 H4B sing 216 n n N2 HN22 H4B sing 217 n n N3 C4 H4B sing 218 n y N3 HN3 H4B sing 219 n n C4 O4 H4B doub 220 n n C4 C4A H4B sing 221 n y C4A C8A H4B doub 222 n y C4A N5 H4B sing 223 n n C8A N8 H4B sing 224 n n N5 C6 H4B sing 225 n n N5 HN5 H4B sing 226 n n N8 C7 H4B sing 227 n n N8 HN8 H4B sing 228 n n C6 C7 H4B sing 229 n n C6 C9 H4B sing 230 n n C6 H6 H4B sing 231 n n C7 H71 H4B sing 232 n n C7 H72 H4B sing 233 n n C9 O9 H4B sing 234 n n C9 C10 H4B sing 235 n n C9 H9 H4B sing 236 n n O9 HO9 H4B sing 237 n n C10 C11 H4B sing 238 n n C10 O10 H4B sing 239 n n C10 H10 H4B sing 240 n n C11 H111 H4B sing 241 n n C11 H112 H4B sing 242 n n C11 H113 H4B sing 243 n n O10 HO0 H4B sing 244 n n # _atom_sites.entry_id 5VVA _atom_sites.fract_transf_matrix[1][1] 0.017461 _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] 0.009438 _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] 0.006435 _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 9OJ A 1 503 800 9OJ 3P8 . F 5 GOL A 1 504 880 GOL GOL . G 6 ZN A 1 505 900 ZN ZN . H 2 HEM B 1 501 500 HEM HEM . I 3 H4B B 1 502 600 H4B BH4 . J 4 9OJ B 1 503 800 9OJ 3P8 . K 5 GOL B 1 504 880 GOL GOL . L 7 HOH A 1 601 13 HOH HOH . L 7 HOH A 2 602 11 HOH HOH . L 7 HOH A 3 603 6 HOH HOH . L 7 HOH A 4 604 12 HOH HOH . L 7 HOH A 5 605 8 HOH HOH . L 7 HOH A 6 606 5 HOH HOH . L 7 HOH A 7 607 10 HOH HOH . L 7 HOH A 8 608 20 HOH HOH . L 7 HOH A 9 609 14 HOH HOH . L 7 HOH A 10 610 17 HOH HOH . L 7 HOH A 11 611 21 HOH HOH . L 7 HOH A 12 612 19 HOH HOH . L 7 HOH A 13 613 9 HOH HOH . L 7 HOH A 14 614 7 HOH HOH . M 7 HOH B 1 601 4 HOH HOH . M 7 HOH B 2 602 15 HOH HOH . M 7 HOH B 3 603 1 HOH HOH . M 7 HOH B 4 604 2 HOH HOH . M 7 HOH B 5 605 3 HOH HOH . M 7 HOH B 6 606 23 HOH HOH . M 7 HOH B 7 607 18 HOH HOH . M 7 HOH B 8 608 16 HOH HOH . M 7 HOH B 9 609 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 N N1 H4B . . . D 3 8.328 12.198 42.46 1 77.45 ? N1 H4B 502 A 1 HETATM 2 C C2 H4B . . . D 3 8.301 12.526 41.153 1 81.91 ? C2 H4B 502 A 1 HETATM 3 N N2 H4B . . . D 3 7.448 11.871 40.333 1 81.56 ? N2 H4B 502 A 1 HETATM 4 N N3 H4B . . . D 3 9.114 13.491 40.661 1 83.61 ? N3 H4B 502 A 1 HETATM 5 C C4 H4B . . . D 3 9.971 14.148 41.472 1 85.36 ? C4 H4B 502 A 1 HETATM 6 O O4 H4B . . . D 3 10.712 15.034 40.986 1 85.61 ? O4 H4B 502 A 1 HETATM 7 C C4A H4B . . . D 3 10.019 13.81 42.824 1 79.21 ? C4A H4B 502 A 1 HETATM 8 C C8A H4B . . . D 3 9.174 12.826 43.303 1 76.36 ? C8A H4B 502 A 1 HETATM 9 N N5 H4B . . . D 3 10.848 14.427 43.69 1 77.02 ? N5 H4B 502 A 1 HETATM 10 N N8 H4B . . . D 3 9.178 12.477 44.612 1 71.98 ? N8 H4B 502 A 1 HETATM 11 C C6 H4B . . . D 3 11.171 13.771 44.947 1 76.19 ? C6 H4B 502 A 1 HETATM 12 C C7 H4B . . . D 3 9.929 13.211 45.619 1 70.02 ? C7 H4B 502 A 1 HETATM 13 C C9 H4B . . . D 3 11.888 14.716 45.906 1 81.85 ? C9 H4B 502 A 1 HETATM 14 O O9 H4B . . . D 3 11.1 15.898 46.09 1 87.3 ? O9 H4B 502 A 1 HETATM 15 C C10 H4B . . . D 3 12.162 14.02 47.242 1 80.88 ? C10 H4B 502 A 1 HETATM 16 C C11 H4B . . . D 3 13.18 14.784 48.078 1 73.78 ? C11 H4B 502 A 1 HETATM 17 O O10 H4B . . . D 3 12.669 12.694 47.02 1 87.79 ? O10 H4B 502 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 38 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 17 #