1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Zhang, D. Fushman, D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking UK Structure STRUE6 2005 0969-2126 23 542 557 10.1016/j.str.2015.01.010 25703377 DNA-Damage-Inducible 1 Protein (Ddi1) Contains an Uncharacteristic Ubiquitin-like Domain that Binds Ubiquitin. 2015 10.2210/pdb2mro/pdb pdb_00002mro 8576.831 Polyubiquitin-B Human Ubiquitin 1 man polymer 4745.367 DNA damage-inducible protein 1 Ubiquitin associated domain, UNP residues 389-428 1 man polymer Ubiquitin v-SNARE-master 1 no no MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG A polypeptide(L) no no GSATFPEQTIKQLMDLGFPRDAVVKALKQTNGNAEFAASLLFQS GSATFPEQTIKQLMDLGFPRDAVVKALKQTNGNAEFAASLLFQS B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n human sample UBB 9606 Homo sapiens 562 Escherichia coli BL21(DE3)pLysS pET3a Baker's yeast ATCC 204508 / S288c sample DDI1, VSM1, YER143W 559292 Saccharomyces cerevisiae 562 Escherichia coli BL21(DE3)pLysS pGEX 4T2 Complex structure based on chemical shift perturbation data and spin-labeling data, calculated using Haddock program database_2 pdbx_database_related pdbx_nmr_sample_details pdbx_nmr_software pdbx_nmr_spectrometer struct_ref_seq_dif database_2 pdbx_database_status repository Initial release Database references Data collection Database references Experimental preparation Database references Other 1 0 2015-02-04 1 1 2015-03-18 1 2 2019-11-06 1 3 2023-06-14 _pdbx_database_related.db_name _pdbx_nmr_sample_details.contents _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _struct_ref_seq_dif.details _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_nmr_data UBIQUITIN NMR STRUCTURE UBA domain of DNA-damage-inducible 1 protein (Ddi1) BMRB Y RCSB 2014-07-14 REL REL REL REL Two titration experiments were conducted. Basically unlabeled ligand protein was added stepwise to N15-Labeled protein solution. structures with the least restraint violations 10 10 2D 1H-15N HSQC 2D 1H-15N HSQC 1 mM [U-100% 15N] 20 mM 7 % [U-99% 2H] 93 % 1 mM [U-100% 15N] 20 mM 7 % [U-99% 2H] 93 % 20 6.8 ambient 298.2 K simulated annealing 1 lowest energy 1 mM [U-100% 15N] Ub-1, 20 mM sodium phosphate-2, 7 % [U-99% 2H] D2O-3, 93 % H2O-4, 93% H2O/7% D2O 93% H2O/7% D2O 1 mM [U-100% 15N] UBA-5, 20 mM sodium phosphate-6, 7 % [U-99% 2H] D2O-7, 93 % H2O-8, 93% H2O/7% D2O 93% H2O/7% D2O Bruker Biospin collection TopSpin 2.1 Bruker Biospin processing TopSpin 2.1 Keller and Wuthrich chemical shift assignment CARA 1.8.1 Alexandre Bonvin geometry optimization HADDOCK 2.1 Alexandre Bonvin refinement HADDOCK 2.1 Alexandre Bonvin structure solution HADDOCK 2.1 600 Bruker AVANCE Bruker Avance MET 1 n 1 MET 1 A GLN 2 n 2 GLN 2 A ILE 3 n 3 ILE 3 A PHE 4 n 4 PHE 4 A VAL 5 n 5 VAL 5 A LYS 6 n 6 LYS 6 A THR 7 n 7 THR 7 A LEU 8 n 8 LEU 8 A THR 9 n 9 THR 9 A GLY 10 n 10 GLY 10 A LYS 11 n 11 LYS 11 A THR 12 n 12 THR 12 A ILE 13 n 13 ILE 13 A THR 14 n 14 THR 14 A LEU 15 n 15 LEU 15 A GLU 16 n 16 GLU 16 A VAL 17 n 17 VAL 17 A GLU 18 n 18 GLU 18 A PRO 19 n 19 PRO 19 A SER 20 n 20 SER 20 A ASP 21 n 21 ASP 21 A THR 22 n 22 THR 22 A ILE 23 n 23 ILE 23 A GLU 24 n 24 GLU 24 A ASN 25 n 25 ASN 25 A VAL 26 n 26 VAL 26 A LYS 27 n 27 LYS 27 A ALA 28 n 28 ALA 28 A LYS 29 n 29 LYS 29 A ILE 30 n 30 ILE 30 A GLN 31 n 31 GLN 31 A ASP 32 n 32 ASP 32 A LYS 33 n 33 LYS 33 A GLU 34 n 34 GLU 34 A GLY 35 n 35 GLY 35 A ILE 36 n 36 ILE 36 A PRO 37 n 37 PRO 37 A PRO 38 n 38 PRO 38 A ASP 39 n 39 ASP 39 A GLN 40 n 40 GLN 40 A GLN 41 n 41 GLN 41 A ARG 42 n 42 ARG 42 A LEU 43 n 43 LEU 43 A ILE 44 n 44 ILE 44 A PHE 45 n 45 PHE 45 A ALA 46 n 46 ALA 46 A GLY 47 n 47 GLY 47 A LYS 48 n 48 LYS 48 A GLN 49 n 49 GLN 49 A LEU 50 n 50 LEU 50 A GLU 51 n 51 GLU 51 A ASP 52 n 52 ASP 52 A GLY 53 n 53 GLY 53 A ARG 54 n 54 ARG 54 A THR 55 n 55 THR 55 A LEU 56 n 56 LEU 56 A SER 57 n 57 SER 57 A ASP 58 n 58 ASP 58 A TYR 59 n 59 TYR 59 A ASN 60 n 60 ASN 60 A ILE 61 n 61 ILE 61 A GLN 62 n 62 GLN 62 A LYS 63 n 63 LYS 63 A GLU 64 n 64 GLU 64 A SER 65 n 65 SER 65 A THR 66 n 66 THR 66 A LEU 67 n 67 LEU 67 A HIS 68 n 68 HIS 68 A LEU 69 n 69 LEU 69 A VAL 70 n 70 VAL 70 A LEU 71 n 71 LEU 71 A ARG 72 n 72 ARG 72 A LEU 73 n 73 LEU 73 A ARG 74 n 74 ARG 74 A GLY 75 n 75 GLY 75 A GLY 76 n 76 GLY 76 A GLY 386 n 1 GLY 386 B SER 387 n 2 SER 387 B ALA 388 n 3 ALA 388 B THR 389 n 4 THR 389 B PHE 390 n 5 PHE 390 B PRO 391 n 6 PRO 391 B GLU 392 n 7 GLU 392 B GLN 393 n 8 GLN 393 B THR 394 n 9 THR 394 B ILE 395 n 10 ILE 395 B LYS 396 n 11 LYS 396 B GLN 397 n 12 GLN 397 B LEU 398 n 13 LEU 398 B MET 399 n 14 MET 399 B ASP 400 n 15 ASP 400 B LEU 401 n 16 LEU 401 B GLY 402 n 17 GLY 402 B PHE 403 n 18 PHE 403 B PRO 404 n 19 PRO 404 B ARG 405 n 20 ARG 405 B ASP 406 n 21 ASP 406 B ALA 407 n 22 ALA 407 B VAL 408 n 23 VAL 408 B VAL 409 n 24 VAL 409 B LYS 410 n 25 LYS 410 B ALA 411 n 26 ALA 411 B LEU 412 n 27 LEU 412 B LYS 413 n 28 LYS 413 B GLN 414 n 29 GLN 414 B THR 415 n 30 THR 415 B ASN 416 n 31 ASN 416 B GLY 417 n 32 GLY 417 B ASN 418 n 33 ASN 418 B ALA 419 n 34 ALA 419 B GLU 420 n 35 GLU 420 B PHE 421 n 36 PHE 421 B ALA 422 n 37 ALA 422 B ALA 423 n 38 ALA 423 B SER 424 n 39 SER 424 B LEU 425 n 40 LEU 425 B LEU 426 n 41 LEU 426 B PHE 427 n 42 PHE 427 B GLN 428 n 43 GLN 428 B SER 429 n 44 SER 429 B author_defined_assembly 2 dimeric 1540 -6 7120 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A O ILE 13 A O ILE 13 A N VAL 5 A N VAL 5 A N PHE 4 A N PHE 4 A O LEU 67 A O LEU 67 A O VAL 70 A O VAL 70 A N ARG 42 A N ARG 42 A N PHE 45 A N PHE 45 A O LYS 48 A O LYS 48 1 A B HZ2 OD2 LYS ASP 6 400 1.57 1 A A OD2 HZ2 ASP LYS 21 29 1.57 2 B B OD1 HZ3 ASP LYS 406 410 1.56 2 A A HZ2 OE2 LYS GLU 11 34 1.58 2 A A HZ3 OD1 LYS ASP 27 52 1.59 2 A B HZ2 OD2 LYS ASP 6 400 1.59 5 A A OD2 HZ1 ASP LYS 21 29 1.54 6 A A H1 OE2 MET GLU 1 16 1.56 6 A B HZ2 OD2 LYS ASP 6 400 1.60 7 A B HZ2 OD2 LYS ASP 6 400 1.59 8 A A OD2 HZ3 ASP LYS 21 29 1.57 8 B B OD2 HZ2 ASP LYS 406 410 1.58 9 A A HZ1 OD2 LYS ASP 27 52 1.56 9 A A OD2 HZ1 ASP LYS 21 29 1.59 10 A A HZ2 OD2 LYS ASP 27 52 1.57 10 A B HZ3 OD2 LYS ASP 6 400 1.59 1 B ASN 416 70.09 63.56 2 A GLU 34 -92.00 -65.27 2 A GLN 62 -106.33 -167.69 3 A THR 9 -79.26 29.84 3 A GLN 62 -114.94 -166.23 4 B SER 387 -143.00 39.88 4 B ASN 416 68.30 62.10 5 A GLN 62 -106.14 -166.60 6 A GLN 62 -101.46 -167.06 6 B ASN 416 61.82 60.85 7 A ARG 42 -160.37 94.51 7 A GLN 62 -109.50 -163.24 7 A ARG 74 -103.36 -63.25 7 B ASN 418 -67.80 93.99 8 A GLN 62 -107.92 -165.99 9 A GLN 62 -113.24 -164.35 9 B ASN 416 61.96 61.10 10 A GLN 62 -110.96 -167.99 10 A GLU 64 70.40 -1.53 lowest energy, model1 Structure of the complex of ubiquitin and the UBA domain from DNA-damage-inducible 1 protein (Ddi1) 1 N N 2 N N A THR 22 A THR 22 HELX_P A GLY 35 A GLY 35 1 1 14 A THR 55 A THR 55 HELX_P A ASN 60 A ASN 60 5 2 6 B PRO 391 B PRO 6 HELX_P B LEU 401 B LEU 16 1 3 11 B PRO 404 B PRO 19 HELX_P B GLN 414 B GLN 29 1 4 11 B ASN 418 B ASN 33 HELX_P B PHE 427 B PHE 42 1 5 10 TRANSPORT PROTEIN/SIGNALING PROTEIN DNA-damage-inducible 1 protein, Ubiquitin associated domain, Ddi1, UBA, HYDROLASE-SIGNALING PROTEIN complex, TRANSPORT PROTEIN-SIGNALING PROTEIN complex UBB_HUMAN UNP 1 1 P0CG47 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG DDI1_YEAST UNP 2 389 P40087 TFPEQTIKQLMDLGFPRDAVVKALKQTNGNAEFAASLLFQ 1 76 2MRO 1 76 P0CG47 A 1 1 76 389 428 2MRO 389 428 P40087 B 2 4 43 2 expression tag GLY 386 2MRO B P40087 UNP 1 2 expression tag SER 387 2MRO B P40087 UNP 2 2 expression tag ALA 388 2MRO B P40087 UNP 3 2 expression tag SER 429 2MRO B P40087 UNP 44 5 anti-parallel parallel anti-parallel anti-parallel A THR 12 A THR 12 A GLU 16 A GLU 16 A GLN 2 A GLN 2 A THR 7 A THR 7 A THR 66 A THR 66 A LEU 71 A LEU 71 A GLN 41 A GLN 41 A PHE 45 A PHE 45 A LYS 48 A LYS 48 A GLN 49 A GLN 49