› 2bgn

X-ray diffraction
3.15Å resolution

HIV-1 Tat protein derived N-terminal nonapeptide Trp2-Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26)

Released:
DOI: 10.2210/pdb2bgn/pdb
PDB entry 2bgn coloured by chain, front view.
PDB entry 2bgn coloured by chain, side view.
PDB entry 2bgn coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of HIV-1 Tat-derived nonapeptides Tat-(1-9) and Trp2-Tat-(1-9) bound to the active site of dipeptidyl-peptidase IV (CD26).
Weihofen WA, Liu J, Reutter W, Saenger W, Fan H
J Biol Chem 280 14911-7 (2005)
PMID: 15695814

Function and Biology Details

Reactions catalysed: 
Release of an N-terminal dipeptide, Xaa-Yaa-|-Zaa-, from a polypeptide, preferentially when Yaa is Pro, provided Zaa is neither Pro nor hydroxyproline.
2'-deoxyadenosine + H(2)O = 2'-deoxyinosine + NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-146249 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (7 distinct):
Dipeptidyl peptidase 4 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 728 amino acids
Theoretical weight: 84.46 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P27487 (Residues: 39-766; Coverage: 95%)
Gene names: ADCP2, CD26, DPP4
Sequence domains:
Structure domains:
Adenosine deaminase Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 363 amino acids
Theoretical weight: 41.09 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P56658 (Residues: 1-363; Coverage: 100%)
Gene name: ADA
Sequence domains: Adenosine deaminase
Structure domains: Metal-dependent hydrolases
Protein Tat Chains: W, X, Y, Z
Molecule details ›
Chains: W, X, Y, Z
Length: 9 amino acids
Theoretical weight: 1.1 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P12506 (Residues: 1-9; Coverage: 11%)
Gene name: tat

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUL
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUL
Carbohydrate polymer
2 bound ligands:
Ligand NAG 14 x NAG
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: C2
Unit cell:
a: 158.945Å b: 170.273Å c: 239.2Å
α: 90° β: 100.93° γ: 90°
R-values:
R R work R free
0.227 0.227 0.247
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

2 review citations

Role of Divalent Cations in HIV-1 Replication and Pathogenicity.
Khan et al. (2020)
1 more

6 mentions without citation

The overlap of small molecule and protein binding sites within families of protein structures.
Davis et al. (2010)
5 more