SMTL ID : 4ej8.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 1 residues within 4Å: Chain A: K.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.70 DMS.2: 4 residues within 4Å: Chain A: G.27, A.28, D.29 Chain B: I.50 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.29 Water bridges: A:D.30 Salt bridges: A:D.29 DMS.3: 6 residues within 4Å: Chain A: R.87, N.88, T.91 Chain B: L.5, W.6 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.87 DMS.7: 3 residues within 4Å: Chain B: G.27, A.28, D.29 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.29 Water bridges: B:D.30 Salt bridges: B:D.29 DMS.8: 5 residues within 4Å: Chain B: R.41, W.42, K.43, Q.58, D.60 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.60

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: E.34, E.35, G.78, P.79, T.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.35 Water bridges: A:P.79 EDO.5: 4 residues within 4Å: Chain A: N.88, T.91, Q.92 Ligands: DMS.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.88 EDO.9: 5 residues within 4Å: Chain B: D.30, K.45, Q.58, T.74, L.76 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain B: P.39, G.40, R.41 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.41, B:R.41

1 x 1F1: 1H-indole-6-carboxylic acid(Non-covalent)

1F1.6: 6 residues within 4Å: Chain A: W.42, P.44, K.45, K.55, V.56, R.57 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.42, A:P.44, A:K.55, A:K.55 Hydrogen bonds: A:K.45, A:V.56, 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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