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PDBsum entry 1yj1
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protein metals Protein-protein interface(s) links
Structural protein PDB id
1yj1

 

 

 

 

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Contents
Protein chains
71 a.a. *
Metals
_CD ×17
_CL ×3
Waters ×230
* Residue conservation analysis
PDB id:
1yj1
Name: Structural protein
Title: X-ray crystal structure of a chemically synthesized [d-gln35]ubiquitin
Structure: Ubiquitin. Chain: a, b, c. Fragment: residues 1-76. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Other_details: the protein was chemically synthesized. The sequence of the protein can be naturally found in homo sapiens (human)
Resolution:
1.30Å     R-factor:   0.196     R-free:   0.218
Authors: D.Bang,G.I.Makhatadze,V.Tereshko,A.A.Kossiakoff,S.B.Kent
Key ref: D.Bang et al. (2005). Total chemical synthesis and X-ray crystal structure of a protein diastereomer: [D-Gln 35]ubiquitin. Angew Chem Int Ed Engl, 44, 3852-3856. PubMed id: 15834850
Date:
13-Jan-05     Release date:   14-Jun-05    
PROCHECK
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 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 71 a.a.
Key:    Secondary structure  CATH domain

 

 
Angew Chem Int Ed Engl 44:3852-3856 (2005)
PubMed id: 15834850  
 
 
Total chemical synthesis and X-ray crystal structure of a protein diastereomer: [D-Gln 35]ubiquitin.
D.Bang, G.I.Makhatadze, V.Tereshko, A.A.Kossiakoff, S.B.Kent.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21058024 J.Sebestik, P.Niederhafner, and J.Jezek (2011).
Peptide and glycopeptide dendrimers and analogous dendrimeric structures and their biomedical applications.
  Amino Acids, 40, 301-370.  
21391285 L.Spasser, K.S.Ajish Kumar, and A.Brik (2011).
Scope and limitation of side-chain assisted ligation.
  J Pept Sci, 17, 252-255.  
21181847 T.Fekner, X.Li, and M.K.Chan (2011).
Nonenzymatic ubiquitylation.
  Chembiochem, 12, 21-33.  
20593472 H.Rohde, and O.Seitz (2010).
Ligation-desulfurization: a powerful combination in the synthesis of peptides and glycopeptides.
  Biopolymers, 94, 551-559.  
20862719 K.S.Kumar, and A.Brik (2010).
Accessing posttranslationally modified proteins through thiol positioning.
  J Pept Sci, 16, 524-529.  
20448897 L.A.Erlich, K.S.Kumar, M.Haj-Yahya, P.E.Dawson, and A.Brik (2010).
N-methylcysteine-mediated total chemical synthesis of ubiquitin thioester.
  Org Biomol Chem, 8, 2392-2396.  
20737108 R.Yang, K.K.Pasunooti, F.Li, X.W.Liu, and C.F.Liu (2010).
Synthesis of K48-linked diubiquitin using dual native chemical ligation at lysine.
  Chem Commun (Camb), 46, 7199-7201.  
20437446 Z.Harpaz, P.Siman, K.S.Kumar, and A.Brik (2010).
Protein synthesis assisted by native chemical ligation at leucine.
  Chembiochem, 11, 1232-1235.  
19772623 S.Annavarapu, and V.Nanda (2009).
Mirrors in the PDB: left-handed alpha-turns guide design with D-amino acids.
  BMC Struct Biol, 9, 61.  
19169452 S.B.Kent (2009).
Total chemical synthesis of proteins.
  Chem Soc Rev, 38, 338-351.  
18523727 N.A.Lakomek, K.F.Walter, C.Farès, O.F.Lange, B.L.de Groot, H.Grubmüller, R.Brüschweiler, A.Munk, S.Becker, J.Meiler, and C.Griesinger (2008).
Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics.
  J Biomol NMR, 41, 139-155.  
17880034 T.Kakizawa, S.Koide-Yoshida, T.Kimura, H.Uchimura, Y.Hayashi, K.Saito, and Y.Kiso (2008).
Fmoc-based solid phase chemical synthesis of 71-meric neuregulin 1-beta1, an epidermal growth factor-like domain.
  J Pept Sci, 14, 261-266.  
16446709 D.Bang, A.V.Gribenko, V.Tereshko, A.A.Kossiakoff, S.B.Kent, and G.I.Makhatadze (2006).
Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis.
  Nat Chem Biol, 2, 139-143.
PDB codes: 2fcm 2fcn 2fcq 2fcs
16639756 D.Bang, B.L.Pentelute, and S.B.Kent (2006).
Kinetically controlled ligation for the convergent chemical synthesis of proteins.
  Angew Chem Int Ed Engl, 45, 3985-3988.  
16453350 G.Roelfes, and H.D.Mootz (2006).
Probing the molecular basis of protein function through chemistry.
  Chembiochem, 7, 545-549.  
16372350 R.B.Davis, and J.T.Lecomte (2006).
A dynamic N-capping motif in cytochrome b5: evidence for a pH-controlled conformational switch.
  Proteins, 63, 336-348.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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