data_8VI8 # _model_server_result.job_id pUFkvcT5LpJyMISvcK_CbA _model_server_result.datetime_utc '2025-04-02 17:11:11' _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 8vi8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":301}' # _entry.id 8VI8 # _exptl.entry_id 8VI8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 438.328 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'AZIDOBIS (DIMETHYLGLYOXIMATO) PYRIDINECOBALT' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.11 _cell.angle_gamma 90 _cell.entry_id 8VI8 _cell.length_a 84.067 _cell.length_b 145.797 _cell.length_c 123.443 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VI8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 ? monomeric 1 author_defined_assembly 5 ? monomeric 1 author_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,G,H,I,J,JA 1 1 B,K,L,M,N,O,KA 2 1 C,P,Q,R,S,T,U,V,LA 3 1 D,W,X,Y,Z,MA 4 1 E,AA,BA,CA,DA,EA,NA 5 1 F,FA,GA,HA,IA,OA 6 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 ? 2 G N N ? 2 K N N ? 2 P N N ? 2 W N N ? 2 AA N N ? 2 FA 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 OH TYR 46 A TYR 43 1_555 CA NA NA . E NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc2 A OD1 ASN 152 A ASN 149 1_555 J NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc3 J NA NA . A NA 304 1_555 JA O HOH . A HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc4 J NA NA . A NA 304 1_655 F OH TYR 46 F TYR 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc5 J NA NA . A NA 304 1_555 OA O HOH . F HOH 402 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc6 JA O HOH . A HOH 409 1_555 CA NA NA . E NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc7 B OH TYR 46 B TYR 43 1_555 U NA NA . C NA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc8 B OD1 ASN 141 B ASN 138 1_555 O NA NA . B NA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc9 B OD1 ASN 152 B ASN 149 1_555 N NA NA . B NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc10 N NA NA . B NA 304 1_555 KA O HOH . B HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc11 N NA NA . B NA 304 3_445 D OH TYR 46 D TYR 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc12 N NA NA . B NA 304 1_555 MA O HOH . D HOH 401 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc13 O NA NA . B NA 305 1_555 KA O HOH . B HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc14 KA O HOH . B HOH 404 1_555 U NA NA . C NA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc15 C OH TYR 46 C TYR 43 1_555 T NA NA . C NA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc16 C OD1 ASN 141 C ASN 138 1_555 V NA NA . C NA 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc17 C OD1 ASN 152 C ASN 149 1_555 U NA NA . C NA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc18 T NA NA . C NA 305 1_555 LA O HOH . C HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc19 T NA NA . C NA 305 3_445 D OD1 ASN 152 D ASN 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc20 T NA NA . C NA 305 1_555 MA O HOH . D HOH 404 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.968 ? metalc ? metalc21 V NA NA . C NA 307 1_555 LA O HOH . C HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc22 D OD1 ASN 141 D ASN 138 1_555 Z NA NA . D NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc23 Z NA NA . D NA 304 1_555 MA O HOH . D HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc24 E OH TYR 46 E TYR 43 1_555 DA NA NA . E NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc25 E OD1 ASN 141 E ASN 138 1_555 EA NA NA . E NA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc26 E OD1 ASN 152 E ASN 149 1_555 CA NA NA . E NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc27 CA NA NA . E NA 303 1_555 NA O HOH . E HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc28 DA NA NA . E NA 304 1_555 NA O HOH . E HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc29 DA NA NA . E NA 304 1_655 F OD1 ASN 152 F ASN 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc30 DA NA NA . E NA 304 1_555 OA O HOH . F HOH 406 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc31 EA NA NA . E NA 305 1_555 NA O HOH . E HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc32 EA NA NA . E NA 305 1_555 NA O HOH . E HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc33 F OD1 ASN 141 F ASN 138 1_555 IA NA NA . F NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc34 IA NA NA . F NA 304 1_555 OA O HOH . F HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc35 IA NA NA . F NA 304 1_555 OA O HOH . F HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? # _chem_comp.formula 'C15 H23 Co N8 O4 1' _chem_comp.formula_weight 438.328 _chem_comp.id X5Z _chem_comp.mon_nstd_flag . _chem_comp.name 'AZIDOBIS (DIMETHYLGLYOXIMATO) PYRIDINECOBALT' _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 C26 C22 X5Z sing 380 n n C27 C23 X5Z sing 381 n n C22 C23 X5Z doub 382 n n C22 N11 X5Z sing 383 n n C23 N12 X5Z sing 384 n n N11 O05 X5Z sing 385 n n N11 CO01 X5Z sing 386 n n N12 O06 X5Z sing 387 n n N12 CO01 X5Z sing 388 n n CO01 N10 X5Z sing 389 n n CO01 N09 X5Z sing 390 n n CO01 N13 X5Z sing 391 n n O04 N10 X5Z sing 392 n n N10 C21 X5Z sing 393 n n O03 N09 X5Z sing 394 n n N09 C20 X5Z sing 395 n n N13 N14 X5Z doub 396 n n C21 C20 X5Z doub 397 n n C21 C25 X5Z sing 398 n n C20 C24 X5Z sing 399 n n N14 N15 X5Z doub 400 n n C24 H1 X5Z sing 401 n n C24 H2 X5Z sing 402 n n C24 H3 X5Z sing 403 n n C25 H4 X5Z sing 404 n n C25 H5 X5Z sing 405 n n C25 H6 X5Z sing 406 n n C26 H7 X5Z sing 407 n n C26 H8 X5Z sing 408 n n C26 H9 X5Z sing 409 n n C27 H10 X5Z sing 410 n n C27 H11 X5Z sing 411 n n C27 H12 X5Z sing 412 n n O03 H14 X5Z sing 413 n n O04 H15 X5Z sing 414 n n O05 H16 X5Z sing 415 n n O06 H17 X5Z sing 416 n n CO01 N1 X5Z sing 417 n n N1 C2 X5Z sing 418 n y C2 C3 X5Z doub 419 n y C3 C4 X5Z sing 420 n y C4 C5 X5Z doub 421 n y C5 C6 X5Z sing 422 n y C6 N1 X5Z doub 423 n y C4 C7 X5Z sing 424 n n C7 C8 X5Z doub 425 n n C2 H18 X5Z sing 426 n n C3 H19 X5Z sing 427 n n C5 H20 X5Z sing 428 n n C6 H21 X5Z sing 429 n n C7 H22 X5Z sing 430 n n C8 H23 X5Z sing 431 n n C8 H24 X5Z sing 432 n n # _atom_sites.entry_id 8VI8 _atom_sites.fract_transf_matrix[1][1] 0.011895 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000023 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006859 _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] 0.008101 _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 G 2 X5Z A 1 301 301 X5Z SM4 . H 3 SO4 A 1 302 2 SO4 SO4 . I 3 SO4 A 1 303 3 SO4 SO4 . J 4 NA A 1 304 2 NA NA . K 2 X5Z B 1 301 301 X5Z SM4 . L 3 SO4 B 1 302 4 SO4 SO4 . M 3 SO4 B 1 303 5 SO4 SO4 . N 4 NA B 1 304 3 NA NA . O 4 NA B 1 305 9 NA NA . P 2 X5Z C 1 301 301 X5Z SM4 . Q 3 SO4 C 1 302 7 SO4 SO4 . R 3 SO4 C 1 303 8 SO4 SO4 . S 3 SO4 C 1 304 9 SO4 SO4 . T 4 NA C 1 305 1 NA NA . U 4 NA C 1 306 4 NA NA . V 4 NA C 1 307 10 NA NA . W 2 X5Z D 1 301 301 X5Z SM4 . X 3 SO4 D 1 302 6 SO4 SO4 . Y 3 SO4 D 1 303 10 SO4 SO4 . Z 4 NA D 1 304 8 NA NA . AA 2 X5Z E 1 301 301 X5Z SM4 . BA 3 SO4 E 1 302 11 SO4 SO4 . CA 4 NA E 1 303 5 NA NA . DA 4 NA E 1 304 6 NA NA . EA 4 NA E 1 305 7 NA NA . FA 2 X5Z F 1 301 301 X5Z SM4 . GA 3 SO4 F 1 302 12 SO4 SO4 . HA 3 SO4 F 1 303 13 SO4 SO4 . IA 4 NA F 1 304 11 NA NA . JA 5 HOH A 1 401 11 HOH HOH . JA 5 HOH A 2 402 12 HOH HOH . JA 5 HOH A 3 403 54 HOH HOH . JA 5 HOH A 4 404 75 HOH HOH . JA 5 HOH A 5 405 9 HOH HOH . JA 5 HOH A 6 406 2 HOH HOH . JA 5 HOH A 7 407 78 HOH HOH . JA 5 HOH A 8 408 6 HOH HOH . JA 5 HOH A 9 409 66 HOH HOH . JA 5 HOH A 10 410 65 HOH HOH . JA 5 HOH A 11 411 76 HOH HOH . JA 5 HOH A 12 412 5 HOH HOH . KA 5 HOH B 1 401 23 HOH HOH . KA 5 HOH B 2 402 17 HOH HOH . KA 5 HOH B 3 403 20 HOH HOH . KA 5 HOH B 4 404 79 HOH HOH . KA 5 HOH B 5 405 80 HOH HOH . KA 5 HOH B 6 406 22 HOH HOH . KA 5 HOH B 7 407 81 HOH HOH . LA 5 HOH C 1 401 77 HOH HOH . LA 5 HOH C 2 402 72 HOH HOH . LA 5 HOH C 3 403 31 HOH HOH . LA 5 HOH C 4 404 24 HOH HOH . LA 5 HOH C 5 405 86 HOH HOH . LA 5 HOH C 6 406 28 HOH HOH . LA 5 HOH C 7 407 27 HOH HOH . LA 5 HOH C 8 408 69 HOH HOH . LA 5 HOH C 9 409 40 HOH HOH . MA 5 HOH D 1 401 19 HOH HOH . MA 5 HOH D 2 402 83 HOH HOH . MA 5 HOH D 3 403 39 HOH HOH . MA 5 HOH D 4 404 70 HOH HOH . MA 5 HOH D 5 405 25 HOH HOH . NA 5 HOH E 1 401 4 HOH HOH . NA 5 HOH E 2 402 85 HOH HOH . NA 5 HOH E 3 403 3 HOH HOH . NA 5 HOH E 4 404 46 HOH HOH . NA 5 HOH E 5 405 47 HOH HOH . NA 5 HOH E 6 406 49 HOH HOH . NA 5 HOH E 7 407 82 HOH HOH . NA 5 HOH E 8 408 68 HOH HOH . NA 5 HOH E 9 409 84 HOH HOH . OA 5 HOH F 1 401 87 HOH HOH . OA 5 HOH F 2 402 7 HOH HOH . OA 5 HOH F 3 403 71 HOH HOH . OA 5 HOH F 4 404 64 HOH HOH . OA 5 HOH F 5 405 50 HOH HOH . OA 5 HOH F 6 406 67 HOH HOH . OA 5 HOH F 7 407 58 HOH HOH . OA 5 HOH F 8 408 55 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 C22 X5Z . . . K 2 48.885 8.639 57.445 1 122.28 ? C22 X5Z 301 B 1 HETATM 2 C C21 X5Z . . . K 2 49.882 10.834 52.769 1 97.5 ? C21 X5Z 301 B 1 HETATM 3 C C20 X5Z . . . K 2 50.26 12.08 53.441 1 113.73 ? C20 X5Z 301 B 1 HETATM 4 C C23 X5Z . . . K 2 49.335 9.854 58.121 1 124.5 ? C23 X5Z 301 B 1 HETATM 5 C C24 X5Z . . . K 2 50.641 13.319 52.688 1 103.23 ? C24 X5Z 301 B 1 HETATM 6 C C25 X5Z . . . K 2 49.951 10.598 51.306 1 85.53 ? C25 X5Z 301 B 1 HETATM 7 C C26 X5Z . . . K 2 48.332 7.449 58.16 1 113.38 ? C26 X5Z 301 B 1 HETATM 8 C C27 X5Z . . . K 2 49.376 9.996 59.597 1 124.3 ? C27 X5Z 301 B 1 HETATM 9 N N09 X5Z . . . K 2 50.221 12.009 54.731 1 122.43 ? N09 X5Z 301 B 1 HETATM 10 N N10 X5Z . . . K 2 49.5 9.913 53.613 1 103.7 ? N10 X5Z 301 B 1 HETATM 11 N N11 X5Z . . . K 2 48.987 8.716 56.167 1 128.38 ? N11 X5Z 301 B 1 HETATM 12 N N12 X5Z . . . K 2 49.693 10.772 57.286 1 124.56 ? N12 X5Z 301 B 1 HETATM 13 N N13 X5Z . . . K 2 51.413 9.612 55.425 1 128.99 ? N13 X5Z 301 B 1 HETATM 14 N N14 X5Z . . . K 2 52.181 10.153 56.045 1 129.53 ? N14 X5Z 301 B 1 HETATM 15 N N15 X5Z . . . K 2 53.086 10.634 56.645 1 128.43 ? N15 X5Z 301 B 1 HETATM 16 O O03 X5Z . . . K 2 50.576 13.027 55.519 1 117.72 ? O03 X5Z 301 B 1 HETATM 17 O O04 X5Z . . . K 2 49.122 8.705 53.204 1 113.17 ? O04 X5Z 301 B 1 HETATM 18 O O05 X5Z . . . K 2 48.622 7.659 55.411 1 123.87 ? O05 X5Z 301 B 1 HETATM 19 O O06 X5Z . . . K 2 50.126 11.964 57.754 1 125.71 ? O06 X5Z 301 B 1 HETATM 20 CO CO01 X5Z . . . K 2 49.598 10.362 55.439 1 129.53 ? CO01 X5Z 301 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 249 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #