data_8QXC # _model_server_result.job_id QPAuljt5_PkKctYqWcJK8w _model_server_result.datetime_utc '2024-10-12 15:29:19' _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 8qxc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":301}' # _entry.id 8QXC # _exptl.entry_id 8QXC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.614 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R,4S)-2-[(1R)-2-[[(5S)-5-acetamido-6-oxidanyl-6-oxidanylidene-hexyl]amino]-2-oxidanylidene-1-(2-phenylethanoylamino)ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid' _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 108.8 _cell.angle_gamma 90 _cell.entry_id 8QXC _cell.length_a 81.566 _cell.length_b 113.236 _cell.length_c 82.873 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8QXC _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,G,I,K 1 1 B,D,H,J,L 2 1 E,F,M,N 3 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 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 disulf ? disulf1 A SG CYS 41 H CYS 41 1_555 A SG CYS 117 H CYS 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 164 H CYS 164 1_555 A SG CYS 220 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 B SG CYS 41 A CYS 41 1_555 B SG CYS 117 A CYS 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf4 B SG CYS 164 A CYS 164 1_555 B SG CYS 220 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf5 C SG CYS 42 L CYS 42 1_555 C SG CYS 107 L CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf6 C SG CYS 153 L CYS 153 1_555 C SG CYS 213 L CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf7 D SG CYS 42 B CYS 42 1_555 D SG CYS 107 B CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf8 D SG CYS 153 B CYS 153 1_555 D SG CYS 213 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? disulf ? disulf9 E SG CYS 41 C CYS 41 1_555 E SG CYS 117 C CYS 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf10 E SG CYS 164 C CYS 164 1_555 E SG CYS 220 C CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf11 F SG CYS 42 D CYS 42 1_555 F SG CYS 107 D CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf12 F SG CYS 153 D CYS 153 1_555 F SG CYS 213 D CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? # _chem_comp.formula 'C24 H34 N4 O7 S' _chem_comp.formula_weight 522.614 _chem_comp.id X5X _chem_comp.mon_nstd_flag . _chem_comp.name '(2R,4S)-2-[(1R)-2-[[(5S)-5-acetamido-6-oxidanyl-6-oxidanylidene-hexyl]amino]-2-oxidanylidene-1-(2-phenylethanoylamino)ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms PenG-Lys # 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 X5X sing 376 n n C2 O1 X5X doub 377 n n C2 N1 X5X sing 378 n n N1 C3 X5X sing 379 n n C3 C4 X5X sing 380 n n C4 C5 X5X sing 381 n n C5 C6 X5X sing 382 n n C6 C7 X5X sing 383 n n C7 N2 X5X sing 384 n n N2 C8 X5X sing 385 n n C8 O2 X5X doub 386 n n C8 C9 X5X sing 387 n n C9 N3 X5X sing 388 n n N3 C10 X5X sing 389 n n C10 O3 X5X doub 390 n n C10 C11 X5X sing 391 n n C11 C12 X5X sing 392 n n C12 C13 X5X doub 393 n y C13 C14 X5X sing 394 n y C14 C15 X5X doub 395 n y C15 C16 X5X sing 396 n y C16 C17 X5X doub 397 n y C9 C18 X5X sing 398 n n C18 N4 X5X sing 399 n n N4 C19 X5X sing 400 n n C19 C20 X5X sing 401 n n C20 O4 X5X doub 402 n n C20 O5 X5X sing 403 n n C19 C21 X5X sing 404 n n C21 C22 X5X sing 405 n n C21 C23 X5X sing 406 n n C21 S1 X5X sing 407 n n C3 C24 X5X sing 408 n n C24 O6 X5X doub 409 n n C24 O7 X5X sing 410 n n C12 C17 X5X sing 411 n y C18 S1 X5X sing 412 n n C4 H7 X5X sing 413 n n C4 H6 X5X sing 414 n n C14 H20 X5X sing 415 n n C5 H9 X5X sing 416 n n C5 H8 X5X sing 417 n n C6 H10 X5X sing 418 n n C6 H11 X5X sing 419 n n C11 H17 X5X sing 420 n n C11 H18 X5X sing 421 n n C7 H12 X5X sing 422 n n C7 H13 X5X sing 423 n n C9 H15 X5X sing 424 n n C13 H19 X5X sing 425 n n N1 H4 X5X sing 426 n n N2 H14 X5X sing 427 n n C3 H5 X5X sing 428 n n N3 H16 X5X sing 429 n n C1 H3 X5X sing 430 n n C1 H1 X5X sing 431 n n C1 H2 X5X sing 432 n n C15 H21 X5X sing 433 n n C16 H22 X5X sing 434 n n C17 H23 X5X sing 435 n n C18 H24 X5X sing 436 n n C19 H26 X5X sing 437 n n C22 H27 X5X sing 438 n n C22 H28 X5X sing 439 n n C22 H29 X5X sing 440 n n C23 H30 X5X sing 441 n n C23 H31 X5X sing 442 n n C23 H32 X5X sing 443 n n N4 H33 X5X sing 444 n n O5 H34 X5X sing 445 n n O7 H35 X5X sing 446 n n # _atom_sites.entry_id 8QXC _atom_sites.fract_transf_matrix[1][1] 0.01226 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004174 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008831 _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] 0.012747 _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 3 X5X H 1 301 301 X5X DRG . H 3 X5X A 1 301 301 X5X DRG . I 4 HOH H 1 401 50 HOH HOH . I 4 HOH H 2 402 65 HOH HOH . I 4 HOH H 3 403 2 HOH HOH . I 4 HOH H 4 404 7 HOH HOH . I 4 HOH H 5 405 28 HOH HOH . I 4 HOH H 6 406 74 HOH HOH . I 4 HOH H 7 407 29 HOH HOH . I 4 HOH H 8 408 58 HOH HOH . I 4 HOH H 9 409 18 HOH HOH . I 4 HOH H 10 410 64 HOH HOH . I 4 HOH H 11 411 17 HOH HOH . I 4 HOH H 12 412 32 HOH HOH . I 4 HOH H 13 413 82 HOH HOH . I 4 HOH H 14 414 8 HOH HOH . I 4 HOH H 15 415 25 HOH HOH . I 4 HOH H 16 416 47 HOH HOH . I 4 HOH H 17 417 39 HOH HOH . I 4 HOH H 18 418 10 HOH HOH . I 4 HOH H 19 419 52 HOH HOH . J 4 HOH A 1 401 85 HOH HOH . J 4 HOH A 2 402 55 HOH HOH . J 4 HOH A 3 403 60 HOH HOH . J 4 HOH A 4 404 86 HOH HOH . J 4 HOH A 5 405 63 HOH HOH . J 4 HOH A 6 406 67 HOH HOH . J 4 HOH A 7 407 87 HOH HOH . J 4 HOH A 8 408 75 HOH HOH . J 4 HOH A 9 409 33 HOH HOH . J 4 HOH A 10 410 57 HOH HOH . J 4 HOH A 11 411 42 HOH HOH . J 4 HOH A 12 412 40 HOH HOH . J 4 HOH A 13 413 66 HOH HOH . J 4 HOH A 14 414 5 HOH HOH . J 4 HOH A 15 415 26 HOH HOH . J 4 HOH A 16 416 38 HOH HOH . J 4 HOH A 17 417 36 HOH HOH . J 4 HOH A 18 418 48 HOH HOH . J 4 HOH A 19 419 46 HOH HOH . J 4 HOH A 20 420 83 HOH HOH . K 4 HOH L 1 301 14 HOH HOH . K 4 HOH L 2 302 1 HOH HOH . K 4 HOH L 3 303 11 HOH HOH . K 4 HOH L 4 304 20 HOH HOH . K 4 HOH L 5 305 56 HOH HOH . K 4 HOH L 6 306 4 HOH HOH . K 4 HOH L 7 307 53 HOH HOH . K 4 HOH L 8 308 12 HOH HOH . K 4 HOH L 9 309 3 HOH HOH . K 4 HOH L 10 310 21 HOH HOH . K 4 HOH L 11 311 22 HOH HOH . K 4 HOH L 12 312 51 HOH HOH . K 4 HOH L 13 313 54 HOH HOH . K 4 HOH L 14 314 61 HOH HOH . K 4 HOH L 15 315 59 HOH HOH . K 4 HOH L 16 316 19 HOH HOH . K 4 HOH L 17 317 13 HOH HOH . K 4 HOH L 18 318 78 HOH HOH . K 4 HOH L 19 319 79 HOH HOH . K 4 HOH L 20 320 6 HOH HOH . K 4 HOH L 21 321 37 HOH HOH . L 4 HOH B 1 301 80 HOH HOH . L 4 HOH B 2 302 44 HOH HOH . L 4 HOH B 3 303 70 HOH HOH . L 4 HOH B 4 304 45 HOH HOH . L 4 HOH B 5 305 34 HOH HOH . L 4 HOH B 6 306 69 HOH HOH . L 4 HOH B 7 307 30 HOH HOH . L 4 HOH B 8 308 41 HOH HOH . L 4 HOH B 9 309 31 HOH HOH . L 4 HOH B 10 310 76 HOH HOH . L 4 HOH B 11 311 35 HOH HOH . M 4 HOH C 1 301 71 HOH HOH . M 4 HOH C 2 302 16 HOH HOH . M 4 HOH C 3 303 72 HOH HOH . M 4 HOH C 4 304 15 HOH HOH . M 4 HOH C 5 305 23 HOH HOH . N 4 HOH D 1 301 81 HOH HOH . N 4 HOH D 2 302 73 HOH HOH . N 4 HOH D 3 303 68 HOH HOH . N 4 HOH D 4 304 27 HOH HOH . N 4 HOH D 5 305 84 HOH HOH . N 4 HOH D 6 306 77 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 C4 X5X . . . G 3 -57.724 31.195 3.084 1 57.88 ? C4 X5X 301 H 1 HETATM 2 C C14 X5X . . . G 3 -62.389 20.932 2.492 1 39.76 ? C14 X5X 301 H 1 HETATM 3 C C5 X5X . . . G 3 -58.703 30.745 2.002 1 58.18 ? C5 X5X 301 H 1 HETATM 4 C C6 X5X . . . G 3 -58.04 30.323 0.694 1 52.82 ? C6 X5X 301 H 1 HETATM 5 C C11 X5X . . . G 3 -62.347 23.608 -0.214 1 38.6 ? C11 X5X 301 H 1 HETATM 6 C C7 X5X . . . G 3 -58.969 29.507 -0.185 1 45.47 ? C7 X5X 301 H 1 HETATM 7 C C8 X5X . . . G 3 -59.627 27.278 0.765 1 45.84 ? C8 X5X 301 H 1 HETATM 8 C C9 X5X . . . G 3 -60.728 26.548 1.527 1 46.25 ? C9 X5X 301 H 1 HETATM 9 C C10 X5X . . . G 3 -62.192 24.81 0.702 1 40.19 ? C10 X5X 301 H 1 HETATM 10 C C12 X5X . . . G 3 -62.153 22.298 0.509 1 39.66 ? C12 X5X 301 H 1 HETATM 11 C C13 X5X . . . G 3 -62.572 22.14 1.829 1 36.69 ? C13 X5X 301 H 1 HETATM 12 N N1 X5X . . . G 3 -56.806 33.134 1.759 1 64.99 ? N1 X5X 301 H 1 HETATM 13 N N2 X5X . . . G 3 -59.789 28.597 0.604 1 49.92 ? N2 X5X 301 H 1 HETATM 14 C C3 X5X . . . G 3 -57.351 32.687 3.027 1 62.26 ? C3 X5X 301 H 1 HETATM 15 N N3 X5X . . . G 3 -60.939 25.248 0.907 1 36.25 ? N3 X5X 301 H 1 HETATM 16 C C1 X5X . . . G 3 -55.902 34.706 0.172 1 63.34 ? C1 X5X 301 H 1 HETATM 17 C C15 X5X . . . G 3 -61.767 19.878 1.851 1 37.25 ? C15 X5X 301 H 1 HETATM 18 C C16 X5X . . . G 3 -61.342 20.018 0.545 1 37.33 ? C16 X5X 301 H 1 HETATM 19 C C17 X5X . . . G 3 -61.541 21.22 -0.126 1 44.05 ? C17 X5X 301 H 1 HETATM 20 C C18 X5X . . . G 3 -60.643 26.667 3.069 1 47.37 ? C18 X5X 301 H 1 HETATM 21 C C19 X5X . . . G 3 -59.074 26.476 4.951 1 40.22 ? C19 X5X 301 H 1 HETATM 22 C C2 X5X . . . G 3 -56.583 34.419 1.494 1 67.21 ? C2 X5X 301 H 1 HETATM 23 C C20 X5X . . . G 3 -58.545 27.58 5.88 1 43.13 ? C20 X5X 301 H 1 HETATM 24 C C21 X5X . . . G 3 -60.371 25.851 5.525 1 45.19 ? C21 X5X 301 H 1 HETATM 25 C C22 X5X . . . G 3 -61.271 26.914 6.117 1 40.82 ? C22 X5X 301 H 1 HETATM 26 C C23 X5X . . . G 3 -60.091 24.761 6.54 1 40.71 ? C23 X5X 301 H 1 HETATM 27 C C24 X5X . . . G 3 -56.322 33.011 4.122 1 60.14 ? C24 X5X 301 H 1 HETATM 28 N N4 X5X . . . G 3 -59.307 26.992 3.597 1 41.71 ? N4 X5X 301 H 1 HETATM 29 O O1 X5X . . . G 3 -56.944 35.337 2.27 1 60.16 ? O1 X5X 301 H 1 HETATM 30 O O2 X5X . . . G 3 -58.691 26.632 0.295 1 42.75 ? O2 X5X 301 H 1 HETATM 31 O O3 X5X . . . G 3 -63.186 25.37 1.186 1 37.51 ? O3 X5X 301 H 1 HETATM 32 O O4 X5X . . . G 3 -57.99 27.207 6.939 1 45.69 ? O4 X5X 301 H 1 HETATM 33 O O5 X5X . . . G 3 -58.723 28.77 5.533 1 45.56 -1 O5 X5X 301 H 1 HETATM 34 O O6 X5X . . . G 3 -56.733 33.617 5.132 1 61.38 ? O6 X5X 301 H 1 HETATM 35 O O7 X5X . . . G 3 -55.136 32.666 3.914 1 57.71 -1 O7 X5X 301 H 1 HETATM 36 S S1 X5X . . . G 3 -61.095 25.188 4.022 1 41.89 ? S1 X5X 301 H 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #