SMTL ID : 4fl8.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

2 x GLN- ILE- IL0- ILE- GLU- ILE- ALA: heptapeptide(Non-covalent)

GLN-ILE-IL0-ILE-GLU-ILE-ALA.1: 29 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, T.80, I.84 Chain B: D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50 Ligands: TYR-ASP-GLN-ILE-IL0-ILE-GLU.2, TYR-ASP-GLN-ILE-IL0-ILE-GLU.2, TYR-ASP-GLN-ILE-IL0-ILE-GLU.2, TYR-ASP-GLN-ILE-IL0-ILE-GLU.2, TYR-ASP-GLN-ILE-IL0-ILE-GLU.2, TYR-ASP-GLN-ILE-IL0-ILE-GLU.2, TYR-ASP-GLN-ILE-IL0-ILE-GLU.2 22 PLIP interactions: 11 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:L.23, A:A.28, A:I.47, A:I.50, A:I.84, B:A.28, B:I.50, B:I.50 Hydrogen bonds: A:D.25, A:D.25, A:G.27, A:D.29, A:G.48, B:G.27, B:D.29, B:D.29, B:D.30, B:G.48, B:G.48 Water bridges: A:G.48, B:I.50, B:I.50 GLN-ILE-IL0-ILE-GLU-ILE-ALA.2: 35 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, K.45, M.46, I.47, G.48, G.49, I.50, V.82, I.84 Ligands: GLN-ILE-IL0-ILE-GLU-ILE-ALA.1, GLN-ILE-IL0-ILE-GLU-ILE-ALA.1, GLN-ILE-IL0-ILE-GLU-ILE-ALA.1, GLN-ILE-IL0-ILE-GLU-ILE-ALA.1, GLN-ILE-IL0-ILE-GLU-ILE-ALA.1, GLN-ILE-IL0-ILE-GLU-ILE-ALA.1, GLN-ILE-IL0-ILE-GLU-ILE-ALA.1, GOL.6 25 PLIP interactions: 14 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:L.23, B:D.30, B:V.82, B:I.84, A:L.23, A:A.28, A:I.50, A:V.82, A:I.84 Hydrogen bonds: B:G.27, B:G.27, B:D.29, B:D.29, B:D.30, B:G.48, B:G.48, A:R.8, A:G.27, A:D.29, A:D.30 Water bridges: B:K.45, B:M.46, A:I.50, A:I.50 Salt bridges: B:K.45

5 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: 3 residues within 4Å: Chain A: Q.18, M.36, S.37 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: R.8, L.10, V.82 Ligands: TYR-ASP-GLN-ILE-IL0-ILE-GLU.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.8 GOL.9: 6 residues within 4Å: Chain B: W.42, K.55, V.56, R.57, V.77, G.78 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.57, B:R.57, B:V.77 Water bridges: B:V.56, B:V.56

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
A

B
B

HIV-1 protease

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