spacer
spacer

PDBsum entry 4dge

Go to PDB code: 
protein Protein-protein interface(s) links
Isomerase/viral protein PDB id
4dge
Jmol
Contents
Protein chains
164 a.a.
136 a.a.
145 a.a.
Waters ×200
PDB id:
4dge
Name: Isomerase/viral protein
Title: Trimcyp cyclophilin domain from macaca mulatta: h70c mutant, ca(o-loop) complex
Structure: Trimcyp. Chain: a, b. Fragment: cyclophilin domain (unp residues 304-468). Synonym: peptidyl-prolyl cis-trans isomerase. Engineered: yes. Mutation: yes. Capsid protein. Chain: c, d. Fragment: cyclophilin-binding domain (unp residues 133-277)
Source: Macaca mulatta. Rhesus macaque. Organism_taxid: 9544. Gene: trimcyp. Expressed in: escherichia coli. Expression_system_taxid: 562. Human immunodeficiency virus 1. HIV-1. Organism_taxid: 11676.
Resolution:
2.20Å     R-factor:   0.189     R-free:   0.255
Authors: M.E.C.Caines,K.Bichel,A.J.Price,W.A.Mcewan,L.C.James
Key ref: M.E.Caines et al. (2012). Diverse HIV viruses are targeted by a conformationally dynamic antiviral. Nat Struct Mol Biol, 19, 411-416. PubMed id: 22407016
Date:
25-Jan-12     Release date:   08-Feb-12    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P62940  (PPIA_MACMU) -  Peptidyl-prolyl cis-trans isomerase A
Seq:
Struc:
165 a.a.
164 a.a.*
Protein chain
Pfam   ArchSchema ?
P12497  (POL_HV1N5) -  Gag-Pol polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1435 a.a.
136 a.a.*
Protein chain
Pfam   ArchSchema ?
P12497  (POL_HV1N5) -  Gag-Pol polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1435 a.a.
145 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 22 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: Chains A, B: E.C.5.2.1.8  - Peptidylprolyl isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylproline (omega=180) = peptidylproline (omega=0)
Peptidylproline (omega=180)
= peptidylproline (omega=0)
   Enzyme class 2: Chains C, D: E.C.2.7.7.49  - RNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
= diphosphate
+ DNA(n+1)
   Enzyme class 3: Chains C, D: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
= diphosphate
+ DNA(n+1)
   Enzyme class 4: Chains C, D: E.C.3.1.13.2  - Exoribonuclease H.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
   Enzyme class 5: Chains C, D: E.C.3.1.26.13  - Retroviral ribonuclease H.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 6: Chains C, D: E.C.3.4.23.16  - HIV-1 retropepsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   4 terms 
  Biological process     viral reproduction   4 terms 
  Biochemical function     isomerase activity     3 terms  

 

 
    reference    
 
 
Nat Struct Mol Biol 19:411-416 (2012)
PubMed id: 22407016  
 
 
Diverse HIV viruses are targeted by a conformationally dynamic antiviral.
M.E.Caines, K.Bichel, A.J.Price, W.A.McEwan, G.J.Towers, B.J.Willett, S.M.Freund, L.C.James.
 
  ABSTRACT  
 
No abstract given.