SMTL ID : 3bva.1

Cystal structure of HIV-1 Active Site Mutant D25N and p2-NC analog inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: K.45, M.46, I.47, F.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.45 Water bridges: A:G.48 GOL.3: 7 residues within 4Å: Chain B: T.12, I.13, K.14, E.65, I.66, A.67, G.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.65, B:A.67, B:G.68 GOL.4: 7 residues within 4Å: Chain B: E.35, K.55, V.56, R.57, V.77, G.78, P.79 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.35, B:R.57 Water bridges: B:V.56, B:V.56

1 x 2NC: N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide(Non-covalent)

2NC.2: 25 residues within 4Å: Chain A: R.8, N.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, V.82, I.84 Chain B: N.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, T.80, P.81, V.82, I.84 29 PLIP interactions: 15 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:A.28, B:I.50, B:I.50, B:P.81, B:I.84, A:D.30, A:I.47, A:I.50, A:I.50, A:V.82, A:I.84 Hydrogen bonds: B:G.27, B:D.29, B:D.29, B:D.30, B:D.30, B:G.48, B:G.48, A:R.8, A:N.25, A:G.27, A:D.29, A:G.48, A:G.48 Water bridges: B:K.45, B:I.50, B:I.50, A:G.48, A:G.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sayer, J.M. et al., Effect of the Active Site D25N Mutation on the Structure, Stability, and Ligand Binding of the Mature HIV-1 Protease. J.Biol.Chem. (2008)

Release Date

2008-04-01

Peptides

Protease (Retropepsin): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease (Retropepsin)

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