SMTL ID : 4e43.1

HIV protease (PR) dimer with acetate in exo site and peptide in active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

1 x ASN- LEU- LEU- GLN- LYS- LYS: Random peptide(Non-covalent)

ASN-LEU-LEU-GLN-LYS-LYS.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, P.81, V.82, I.84 Chain B: D.25, G.27, A.28, D.29, D.30, K.45, M.46, I.47, G.48, G.49, I.50, F.53, P.81, V.82 Ligands: GOL.13 27 PLIP interactions: 15 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:A.28, B:I.47, B:P.81, B:V.82, A:L.23, A:I.50, A:P.81, A:V.82 Hydrogen bonds: B:G.27, B:D.29, B:D.29, B:D.30, B:D.30, B:D.30, B:G.48, B:G.48, B:I.50, A:G.27, A:D.29, A:D.30, A:D.30, A:D.30, A:G.48 Water bridges: B:G.49, B:R.87, A:R.8, A:I.50

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

DMS.2: 6 residues within 4Å: Chain A: R.87, N.88, T.91 Chain B: L.5, W.6 Ligands: DMS.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.87, A:R.87 DMS.3: 5 residues within 4Å: Chain A: G.73, T.74, N.88 Ligands: DMS.2, GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.74, A:T.74, A:N.88 DMS.9: 6 residues within 4Å: Chain B: E.35, K.55, V.56, R.57, V.77, G.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.57 Salt bridges: B:E.35 DMS.10: 5 residues within 4Å: Chain A: G.94, T.96 Chain B: Q.2, T.4 Ligands: GOL.6 No protein-ligand interaction detected (PLIP)

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

ACT.4: 7 residues within 4Å: Chain A: K.14, I.15, G.16, G.17, L.63, E.65 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.14, A:E.65 Hydrogen bonds: A:G.16, A:G.17

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: I.15, G.16, P.39, I.62, L.63 Ligands: ACT.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.16, A:L.63, A:L.63 GOL.6: 4 residues within 4Å: Chain A: Q.92, I.93, G.94 Ligands: DMS.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.92 GOL.7: 2 residues within 4Å: Chain A: P.1, Q.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.2 GOL.8: 4 residues within 4Å: Chain A: K.43, Q.58, D.60 Ligands: DMS.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.43, A:K.43, A:Q.58 GOL.12: 4 residues within 4Å: Chain A: W.6 Chain B: R.87, N.88, T.91 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.87, B:R.87, B:T.91, B:T.91 GOL.13: 6 residues within 4Å: Chain B: D.29, D.30, Q.58, T.74, N.88 Ligands: ASN-LEU-LEU-GLN-LYS-LYS.1 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.30, B:T.74, B:N.88 Water bridges: B:T.31, B:Q.58, B:Q.58, B:Q.58, B:Q.58, B:T.74 GOL.14: 6 residues within 4Å: Chain B: R.41, W.42, K.43, Q.58, Y.59, D.60 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.58, B:D.60, B:D.60 Water bridges: B:R.41, B:W.42 GOL.15: 7 residues within 4Å: Chain A: T.4, L.5, W.6 Chain B: T.91, G.94, C.95, T.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.5 GOL.16: 7 residues within 4Å: Chain B: I.15, G.16, L.38, P.39, I.62, L.63 Ligands: GOL.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.16, B:L.63 GOL.17: 8 residues within 4Å: Chain B: K.14, G.16, G.17, L.63, I.64, E.65, K.70 Ligands: GOL.16 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.14, B:G.17, B:L.63, B:E.65, B:K.70, B:K.70 Water bridges: B:A.71

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.11: 5 residues within 4Å: Chain B: T.12, L.19, E.65, C.67, G.68 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perryman, A.L. et al., Fragment-based screen against HIV protease. Chem.Biol.Drug Des. (2010)

Release Date

2012-05-30

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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