SMTL ID : 3o9h.1

Crystal Structure of wild-type HIV-1 Protease in complex with kd26

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 2 residues within 4Å: Chain A: M.36, N.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37, A:N.37 PO4.2: 3 residues within 4Å: Chain A: G.68, H.69, K.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.69, A:K.70, A:K.70 PO4.3: 2 residues within 4Å: Chain A: K.7, R.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.8 Water bridges: A:R.8, A:R.8 PO4.4: 3 residues within 4Å: Chain A: R.14, G.16, G.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.17 Water bridges: A:G.16, A:G.16 Salt bridges: A:R.14

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

ACT.5: 3 residues within 4Å: Chain A: K.20, E.21, N.83 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.21, A:E.21, A:N.83 Salt bridges: A:K.20

1 x K2E: (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-ethylbutyl)amino]-1-benzyl-2-hydroxypropyl}carbamate(Non-covalent)

K2E.6: 25 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, G.48, G.49, I.50, T.80, V.82, I.84 Chain B: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, P.81, I.84 20 PLIP interactions: 10 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:L.23, B:A.28, B:V.32, B:P.81, B:I.84, A:V.82, A:I.84 Hydrogen bonds: B:D.29, B:D.30, A:D.25, A:G.27, A:G.27, A:D.29, A:D.30 Water bridges: B:G.48, B:G.48, A:I.50, A:I.50 Salt bridges: B:D.25, A:D.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nalam, M.N. et al., Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance. Chem.Biol. (2013)

Release Date

2011-08-10

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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