SMTL ID : 2a1e.1

High resolution structure of HIV-1 PR with TS-126

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 6 residues within 4Å: Chain A: R.87, N.88, T.91, Q.92 Chain B: L.5, W.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.91 DMS.2: 3 residues within 4Å: Chain A: G.73, T.74, N.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.74, A:N.88 DMS.3: 3 residues within 4Å: Chain A: Q.18, L.19, K.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.18, A:K.20 DMS.4: 9 residues within 4Å: Chain A: T.12, I.13, K.14, L.19, E.65, I.66, A.67, G.68, H.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.68 Salt bridges: A:E.65 DMS.10: 7 residues within 4Å: Chain B: E.35, K.55, V.56, R.57, V.77, G.78, P.79 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.57 Salt bridges: B:E.35

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

NA.5: 2 residues within 4Å: Chain B: K.14, E.65 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.65 Water bridges: B:K.14

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

CL.6: 2 residues within 4Å: Chain B: T.4, W.6 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 5 residues within 4Å: Chain A: L.5, W.6 Chain B: R.87, N.88, T.91 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.6 Hydrogen bonds: B:T.91 Water bridges: B:R.87 Salt bridges: B:R.87 ACT.8: 2 residues within 4Å: Chain B: P.39, G.40 No protein-ligand interaction detected (PLIP)

1 x IPF: N-ACETYLTRYPTOPHYL-N~1~-{3-[1-(N-ACETYLTRYPTOPHYLVALYL)PYRROLIDIN-2-YL]-1-BENZYL-2,3-DIHYDROXYPROPYL}VALINAMIDE(Non-covalent)

IPF.9: 36 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, K.45, I.47, G.48, G.49, I.50, F.53, P.81, V.82, I.84 Chain B: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, K.45, M.46, I.47, G.48, G.49, I.50, F.53, L.76, P.81, V.82, I.84 30 PLIP interactions: 16 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:L.23, B:A.28, B:F.53, B:P.81, A:L.23, A:V.32, A:I.47, A:I.50, A:P.81, A:V.82, A:I.84 Hydrogen bonds: B:R.8, B:D.25, B:D.25, B:G.27, B:G.27, B:D.29, B:D.29, B:G.48, B:G.48, A:D.29, A:D.29, A:G.48, A:G.48 Water bridges: B:R.8, B:R.8, B:I.50, A:R.8, A:R.8, A:I.50

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain B: T.12, I.13, K.14, L.19, E.65, I.66, A.67, G.68 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.14, 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

Geremia, S. et al., A potent HIV protease inhibitor identified in an epimeric mixture by high-resolution protein crystallography. Chemmedchem (2006)

Release Date

2006-02-21

Peptides

Pol polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pol polyprotein

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