SMTL ID : 4fm6.1

HIV-1 protease mutant V32I complexed with reaction intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

1 x TYR- ASP- GLN- ILE- ILE: hexapeptide(Non-covalent)

TYR-ASP-GLN-ILE-ILE.1: 21 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, I.50, V.82, I.84 Chain B: D.25, G.27, A.28, D.29, D.30, I.32, K.45, M.46, I.47, G.48, G.49, I.50, F.53, I.84 20 PLIP interactions: 15 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.28, B:I.32, B:I.47, B:F.53, B:I.84, A:L.23, A:I.50, A:V.82, A:I.84 Hydrogen bonds: B:G.27, B:D.29, B:D.29, B:D.29, B:G.48, B:G.48, A:R.8 Water bridges: B:K.45, B:M.46, B:I.50 Salt bridges: B:K.45

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 1 residues within 4Å: Chain A: D.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.60, A:D.60 Water bridges: A:R.41

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: G.73, T.74, N.88 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: K.7, R.8 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: T.4, L.5, W.6, K.7 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain B: R.41 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain B: T.12, I.13, E.65, I.66, A.67, G.68 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.65, B:E.65, B:A.67, B:G.68 Water bridges: B:T.12, B:T.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, C.H. et al., Capturing the Reaction Pathway in Near-Atomic-Resolution Crystal Structures of HIV-1 Protease. Biochemistry (2012)

Release Date

2012-10-17

Peptides

HIV-1 protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

HIV-1 protease

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