SMTL ID : 3b7v.1

HIV-1 protease complexed with gem-diol-amine tetrahedral intermediate NLLTQI

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-dimer

Ligands

1 x ASN- LEU- LNT- GLN- ILE: peptide(Non-covalent)

ASN-LEU-LNT-GLN-ILE.1: 27 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, V.82, I.84 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, F.53, P.81, V.82, I.84 26 PLIP interactions: 11 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:A.28, A:I.47, A:I.50, B:L.23, B:I.47, B:F.53, B:P.81, B:V.82, B:I.84 Hydrogen bonds: A:G.27, A:G.27, A:D.29, A:G.48, B:G.27, B:G.27, B:D.29, B:D.29, B:D.30, B:D.30, B:G.48, B:G.48 Water bridges: A:R.8, A:G.48, A:G.48, A:I.50, B:I.50

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

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

3 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: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain B: P.1, A.67, H.69 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovalevsky, A.Y. et al., Caught in the Act: The 1.5 A Resolution Crystal Structures of the HIV-1 Protease and the I54V Mutant Reveal a Tetrahedral Reaction Intermediate. Biochemistry (2007)

Release Date

2007-12-18

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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