SMTL ID : 2nnp.1

Crystal structure analysis of HIV-1 protease mutant I84V with a inhibitor saquinavir

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

1 x ROC: (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide(Non-covalent)

ROC.1: 26 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, T.80, P.81, V.82 Chain B: R.8, L.23, D.25, G.27, A.28, D.30, V.32, I.47, G.48, G.49, I.50, P.81, V.82, V.84 25 PLIP interactions: 11 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:I.50, A:P.81, A:V.82, B:L.23, B:A.28, B:V.32, B:I.47, B:I.50, B:P.81, B:V.82, B:V.82, B:V.84 Hydrogen bonds: A:G.27, A:G.27, A:D.29, A:D.30, A:D.30, A:G.48 Water bridges: A:G.48, B:G.27, B:D.29, B:I.50, B:I.50 Salt bridges: A:D.25, B:D.25

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 2 residues within 4Å: Chain A: K.7, R.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.8 Salt bridges: A:K.7, A:R.8 ACY.6: 2 residues within 4Å: Chain B: M.36, S.37 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.37 Water bridges: B:S.37

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: L.5, W.6 Chain B: D.29, R.87, N.88, T.91 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.87, B:R.87, B:R.87 Water bridges: B:D.30, B:D.30, B:T.91, B:T.91 GOL.4: 1 residues within 4Å: Chain A: K.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.55

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 1 residues within 4Å: Chain B: R.57 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tie, Y. et al., Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir. Proteins (2007)

Release Date

2007-03-13

Peptides

PROTEASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTEASE

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