SMTL ID : 4ejl.1

Apo HIV Protease (PR) dimer in closed form with fragment 1F1-N in the outside/top of flap

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 6 residues within 4Å: Chain A: D.29, R.87, N.88, T.91, Q.92 Chain B: W.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.29, A:R.87, A:Q.92

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 4 residues within 4Å: Chain A: P.1, Q.2 Chain B: N.98, F.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.98, B:F.99 DMS.7: 7 residues within 4Å: Chain B: K.14, I.15, G.16, G.17, I.63, I.64, E.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.16, B:G.17 Salt bridges: B:E.65

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: D.25, G.27, I.50 Chain B: D.25, G.27 Ligands: GOL.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.27, B:G.27 Water bridges: B:I.50 GOL.4: 6 residues within 4Å: Chain A: A.28, D.29, D.30, G.48 Chain B: I.50 Ligands: GOL.3 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.29, A:D.30, A:D.30, A:D.30, A:G.48 Water bridges: B:I.50 GOL.5: 5 residues within 4Å: Chain A: I.15, G.16, P.39, I.62, I.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.16, A:I.63 GOL.8: 2 residues within 4Å: Chain B: P.44, K.55 No protein-ligand interaction detected (PLIP)

1 x IOP: INDOLYLPROPIONIC ACID(Non-covalent)

IOP.6: 6 residues within 4Å: Chain A: W.42, P.44, K.45, K.55, V.56, R.57 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.42, A:K.55, A:K.55, A:R.57 Hydrogen bonds: A:K.45, A:V.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tiefenbrunn, T. et al., Small molecule regulation of protein conformation by binding in the Flap of HIV protease. Acs Chem.Biol. (2013)

Release Date

2013-05-01

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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