data_8J83 # _model_server_result.job_id 3FFegJjtCLi7Rse88idiWg _model_server_result.datetime_utc '2025-03-04 08:32:01' _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 8j83 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 8J83 # _exptl.entry_id 8J83 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 740.557 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE' _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 106.72 _cell.angle_gamma 90 _cell.entry_id 8J83 _cell.length_a 232.86 _cell.length_b 73.95 _cell.length_c 95.74 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8J83 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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,N,O,P,Q,R,S _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 C N N ? 3 D 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 SG CYS 102 A CYS 102 1_555 F FE1 FES . A FES 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc2 A SG CYS 115 A CYS 115 1_555 F FE1 FES . A FES 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc3 A SG CYS 118 A CYS 118 1_555 F FE2 FES . A FES 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc4 A SG CYS 132 A CYS 132 1_555 F FE2 FES . A FES 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc5 A SG CYS 213 A CYS 213 1_555 G FE2 SF4 . A SF4 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc6 A SG CYS 216 A CYS 216 1_555 G FE1 SF4 . A SF4 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc7 A SG CYS 219 A CYS 219 1_555 G FE4 SF4 . A SF4 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc8 A SG CYS 223 A CYS 223 1_555 H FE4 SF4 . A SF4 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc9 A SG CYS 256 A CYS 256 1_555 H FE2 SF4 . A SF4 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc10 A SG CYS 259 A CYS 259 1_555 H FE3 SF4 . A SF4 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc11 A SG CYS 262 A CYS 262 1_555 H FE1 SF4 . A SF4 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc12 A SG CYS 266 A CYS 266 1_555 G FE3 SF4 . A SF4 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc13 A SG CYS 295 A CYS 295 1_555 I FE1 SF4 . A SF4 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc14 A SG CYS 298 A CYS 298 1_555 I FE3 SF4 . A SF4 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc15 A SG CYS 302 A CYS 302 1_555 I FE4 SF4 . A SF4 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc16 A SG CYS 329 A CYS 329 1_555 I FE2 SF4 . A SF4 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc17 A SG CYS 436 A CYS 436 1_555 E W W . A W 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc18 C S12 MGD . A MGD 1001 1_555 E W W . A W 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc19 C S13 MGD . A MGD 1001 1_555 E W W . A W 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc20 D S12 MGD . A MGD 1002 1_555 E W W . A W 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc21 D S13 MGD . A MGD 1002 1_555 E W W . A W 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc22 E W W . A W 1003 1_555 S O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc23 B SG CYS 113 B CYS 113 1_555 P FE1 FES . B FES 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc24 B SG CYS 118 B CYS 118 1_555 P FE1 FES . B FES 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc25 B SG CYS 146 B CYS 146 1_555 P FE2 FES . B FES 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc26 B SG CYS 150 B CYS 150 1_555 P FE2 FES . B FES 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc27 B SG CYS 502 B CYS 502 1_555 O FE2 SF4 . B SF4 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc28 B SG CYS 505 B CYS 505 1_555 O FE3 SF4 . B SF4 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc29 B SG CYS 508 B CYS 508 1_555 O FE1 SF4 . B SF4 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc30 B SG CYS 542 B CYS 542 1_555 O FE4 SF4 . B SF4 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? # _chem_comp.formula 'C20 H26 N10 O13 P2 S2' _chem_comp.formula_weight 740.557 _chem_comp.id MGD _chem_comp.mon_nstd_flag . _chem_comp.name '2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE' # 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 PB O1B MGD doub 308 n n PB O2B MGD sing 309 n n PB O3B MGD sing 310 n n PB O5' MGD sing 311 n n O2B HOB2 MGD sing 312 n n O3B PA MGD sing 313 n n O3A PA MGD sing 314 n n O3A C10 MGD sing 315 n n PA O1A MGD doub 316 n n PA O2A MGD sing 317 n n O2A HOA2 MGD sing 318 n n O5' C5' MGD sing 319 n n C5' C4' MGD sing 320 n n C5' "H5'1" MGD sing 321 n n C5' "H5'2" MGD sing 322 n n C4' O4' MGD sing 323 n n C4' C3' MGD sing 324 n n C4' H4' MGD sing 325 n n O4' C1' MGD sing 326 n n C3' O3' MGD sing 327 n n C3' C2' MGD sing 328 n n C3' H3' MGD sing 329 n n O3' HO3' MGD sing 330 n n C2' O2' MGD sing 331 n n C2' C1' MGD sing 332 n n C2' H2' MGD sing 333 n n O2' HO2' MGD sing 334 n n C1' N9 MGD sing 335 n n C1' H1' MGD sing 336 n n N9 C8 MGD sing 337 n y N9 C4 MGD sing 338 n y C8 N7 MGD doub 339 n y C8 H8 MGD sing 340 n n N7 C5 MGD sing 341 n y C5 C6 MGD sing 342 n n C5 C4 MGD doub 343 n y C6 O6 MGD doub 344 n n C6 N1 MGD sing 345 n n N1 C2 MGD sing 346 n n N1 HN1 MGD sing 347 n n C2 N2 MGD sing 348 n n C2 N3 MGD doub 349 n n N2 HN21 MGD sing 350 n n N2 HN22 MGD sing 351 n n N3 C4 MGD sing 352 n n C10 C11 MGD sing 353 n n C10 H101 MGD sing 354 n n C10 H102 MGD sing 355 n n C11 O11 MGD sing 356 n n C11 C12 MGD sing 357 n n C11 H11 MGD sing 358 n n O11 C23 MGD sing 359 n n C12 S12 MGD sing 360 n n C12 C13 MGD doub 361 n n S12 H12 MGD sing 362 n n C13 S13 MGD sing 363 n n C13 C14 MGD sing 364 n n S13 H13 MGD sing 365 n n C14 N15 MGD sing 366 n n C14 C23 MGD sing 367 n n C14 H14 MGD sing 368 n n N15 C16 MGD sing 369 n n N15 H15 MGD sing 370 n n C16 C17 MGD sing 371 n n C16 C21 MGD doub 372 n n C17 O17 MGD doub 373 n n C17 N18 MGD sing 374 n n N18 C19 MGD sing 375 n n N18 H18 MGD sing 376 n n C19 N19 MGD sing 377 n n C19 N20 MGD doub 378 n n N19 H191 MGD sing 379 n n N19 H192 MGD sing 380 n n N20 C21 MGD sing 381 n n C21 N22 MGD sing 382 n n N22 C23 MGD sing 383 n n N22 H22 MGD sing 384 n n C23 H23 MGD sing 385 n n # _atom_sites.entry_id 8J83 _atom_sites.fract_transf_matrix[1][1] 0.004294 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00129 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013523 _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] 0.010906 _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 3 MGD A 1 1001 1001 MGD MGD . D 3 MGD A 1 1002 1002 MGD MGD . E 4 W A 1 1003 1003 W W . F 5 FES A 1 1004 1011 FES FES . G 6 SF4 A 1 1005 1012 SF4 SF4 . H 6 SF4 A 1 1006 1013 SF4 SF4 . I 6 SF4 A 1 1007 1014 SF4 SF4 . J 7 GOL A 1 1008 1015 GOL GOL . K 7 GOL A 1 1009 1021 GOL GOL . L 8 PEG A 1 1010 1022 PEG PEG . M 7 GOL A 1 1011 607 GOL GOL . N 9 FMN B 1 601 601 FMN FMN . O 6 SF4 B 1 602 602 SF4 SF4 . P 5 FES B 1 603 603 FES FES . Q 7 GOL B 1 604 608 GOL GOL . R 7 GOL B 1 605 609 GOL GOL . S 10 HOH A 1 1101 1020 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 PB MGD . . . C 3 -58.373 51.22 57.856 1 43.25 ? PB MGD 1001 A 1 HETATM 2 O O1B MGD . . . C 3 -59.282 50.673 56.768 1 42.97 ? O1B MGD 1001 A 1 HETATM 3 O O2B MGD . . . C 3 -56.922 51.276 57.389 1 42.11 ? O2B MGD 1001 A 1 HETATM 4 O O3B MGD . . . C 3 -58.511 50.297 59.237 1 42.7 ? O3B MGD 1001 A 1 HETATM 5 O O3A MGD . . . C 3 -57.679 49.706 61.68 1 42.87 ? O3A MGD 1001 A 1 HETATM 6 P PA MGD . . . C 3 -58.171 50.957 60.729 1 40.5 ? PA MGD 1001 A 1 HETATM 7 O O1A MGD . . . C 3 -57.076 51.984 60.591 1 42.91 ? O1A MGD 1001 A 1 HETATM 8 O O2A MGD . . . C 3 -59.38 51.59 61.358 1 42.95 ? O2A MGD 1001 A 1 HETATM 9 O O5' MGD . . . C 3 -58.87 52.754 58.274 1 43.71 ? O5' MGD 1001 A 1 HETATM 10 C C5' MGD . . . C 3 -58.346 53.839 57.53 1 44.05 ? C5' MGD 1001 A 1 HETATM 11 C C4' MGD . . . C 3 -59.552 54.821 57.295 1 44.01 ? C4' MGD 1001 A 1 HETATM 12 O O4' MGD . . . C 3 -58.973 56.198 56.93 1 44.71 ? O4' MGD 1001 A 1 HETATM 13 C C3' MGD . . . C 3 -60.256 54.446 56.3 1 44.14 ? C3' MGD 1001 A 1 HETATM 14 O O3' MGD . . . C 3 -61.679 54.573 56.648 1 43.74 ? O3' MGD 1001 A 1 HETATM 15 C C2' MGD . . . C 3 -59.89 55.429 55.012 1 44.14 ? C2' MGD 1001 A 1 HETATM 16 O O2' MGD . . . C 3 -61.104 55.633 54.239 1 44.03 ? O2' MGD 1001 A 1 HETATM 17 C C1' MGD . . . C 3 -59.558 56.537 55.532 1 44.61 ? C1' MGD 1001 A 1 HETATM 18 N N9 MGD . . . C 3 -58.455 57.255 54.879 1 43.82 ? N9 MGD 1001 A 1 HETATM 19 C C8 MGD . . . C 3 -57.654 56.619 54.013 1 43.65 ? C8 MGD 1001 A 1 HETATM 20 N N7 MGD . . . C 3 -56.726 57.513 53.61 1 43.88 ? N7 MGD 1001 A 1 HETATM 21 C C5 MGD . . . C 3 -56.949 58.666 54.236 1 43.99 ? C5 MGD 1001 A 1 HETATM 22 C C6 MGD . . . C 3 -56.265 60.033 54.216 1 44.56 ? C6 MGD 1001 A 1 HETATM 23 O O6 MGD . . . C 3 -55.319 60.218 53.528 1 44.9 ? O6 MGD 1001 A 1 HETATM 24 N N1 MGD . . . C 3 -56.767 61.089 55.025 1 45.11 ? N1 MGD 1001 A 1 HETATM 25 C C2 MGD . . . C 3 -57.921 60.86 55.866 1 44.96 ? C2 MGD 1001 A 1 HETATM 26 N N2 MGD . . . C 3 -58.455 61.888 56.702 1 45.47 ? N2 MGD 1001 A 1 HETATM 27 N N3 MGD . . . C 3 -58.562 59.57 55.881 1 44.56 ? N3 MGD 1001 A 1 HETATM 28 C C4 MGD . . . C 3 -58.026 58.483 55.031 1 44.19 ? C4 MGD 1001 A 1 HETATM 29 C C10 MGD . . . C 3 -56.657 48.832 61.23 1 42.54 ? C10 MGD 1001 A 1 HETATM 30 C C11 MGD . . . C 3 -56.494 47.919 62.369 1 42.49 ? C11 MGD 1001 A 1 HETATM 31 O O11 MGD . . . C 3 -57.372 46.734 62.132 1 42.41 ? O11 MGD 1001 A 1 HETATM 32 C C12 MGD . . . C 3 -55.062 47.435 62.553 1 42.7 ? C12 MGD 1001 A 1 HETATM 33 S S12 MGD . . . C 3 -53.604 48.308 61.938 1 43.72 ? S12 MGD 1001 A 1 HETATM 34 C C13 MGD . . . C 3 -54.911 45.807 62.589 1 42.71 ? C13 MGD 1001 A 1 HETATM 35 S S13 MGD . . . C 3 -53.187 45.286 62.436 1 43.63 ? S13 MGD 1001 A 1 HETATM 36 C C14 MGD . . . C 3 -55.869 45.065 63.155 1 43 ? C14 MGD 1001 A 1 HETATM 37 N N15 MGD . . . C 3 -55.936 43.964 62.423 1 42.8 ? N15 MGD 1001 A 1 HETATM 38 C C16 MGD . . . C 3 -56.96 43.153 62.636 1 42.85 ? C16 MGD 1001 A 1 HETATM 39 C C17 MGD . . . C 3 -56.848 41.709 62.3 1 42.62 ? C17 MGD 1001 A 1 HETATM 40 O O17 MGD . . . C 3 -55.836 41.269 61.863 1 42.77 ? O17 MGD 1001 A 1 HETATM 41 N N18 MGD . . . C 3 -58.025 40.773 62.516 1 43.1 ? N18 MGD 1001 A 1 HETATM 42 C C19 MGD . . . C 3 -59.372 41.466 63.114 1 42.72 ? C19 MGD 1001 A 1 HETATM 43 N N19 MGD . . . C 3 -60.578 40.705 63.387 1 43.44 ? N19 MGD 1001 A 1 HETATM 44 N N20 MGD . . . C 3 -59.329 42.986 63.404 1 42.86 ? N20 MGD 1001 A 1 HETATM 45 C C21 MGD . . . C 3 -58.169 43.737 63.156 1 42.77 ? C21 MGD 1001 A 1 HETATM 46 N N22 MGD . . . C 3 -58.225 45.069 63.443 1 42.57 ? N22 MGD 1001 A 1 HETATM 47 C C23 MGD . . . C 3 -57.13 45.785 63.222 1 42.74 ? C23 MGD 1001 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 47 #