SMTL ID : 4tvg.1

HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment AK-2097 in the outside/top of flap

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

1 x IVA- VAL- VAL- STA- ALA- STA: Pepstatin(Non-covalent)

IVA-VAL-VAL-STA-ALA-STA.1: 26 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, P.81, I.84 Chain B: R.8, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, T.80, V.82, I.84 25 PLIP interactions: 13 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:V.32, A:I.47, A:I.47, A:I.50, A:P.81, A:I.84, B:A.28, B:I.50, B:I.50, B:V.82, B:I.84 Hydrogen bonds: A:D.25, A:G.27, A:D.29, A:D.29, A:G.48, A:G.48, A:I.50, B:G.27, B:D.29, B:D.30, B:G.48, B:G.48 Water bridges: B:K.45 Salt bridges: B:K.45

1 x K97: 3-(morpholin-4-ylmethyl)-1H-indole-6-carboxylic acid(Non-covalent)

K97.2: 6 residues within 4Å: Chain A: P.44, K.45, M.46, K.55, V.56, R.57 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.44 Hydrogen bonds: A:K.45, A:V.56, A:V.56

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain B: P.44, K.45, M.46 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, N. et al., Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease. J.Phys.Chem.B (2015)

Release Date

2014-09-24

Peptides

HIV Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV Protease

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