SMTL ID : 3o9b.1

Crystal Structure of wild-type HIV-1 Protease in Complex with kd25

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: R.14, G.16, G.17, P.63 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.16, A:G.17 Salt bridges: A:R.14 PO4.2: 2 residues within 4Å: Chain A: M.36, N.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.37, A:N.37 Water bridges: A:Q.18 PO4.7: 3 residues within 4Å: Chain B: R.14, E.65, G.68 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.14, B:G.68, B:G.68 Salt bridges: B:R.14

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: G.48, G.49, G.52, F.53 Chain B: P.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.48

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

ACT.4: 3 residues within 4Å: Chain A: R.14, G.17, L.19 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.14 ACT.5: 3 residues within 4Å: Chain A: K.20, E.21, N.83 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.21, A:E.21, A:N.83 Water bridges: A:K.20 Salt bridges: A:K.20

1 x K2A: (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-({[4-(hydroxymethyl)phenyl]sulfonyl}[(2S)-2-methylbutyl]amino)propyl]carbamate(Non-covalent)

K2A.6: 25 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.50, P.81, V.82 Chain B: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.50, P.81, V.82, I.84 19 PLIP interactions: 10 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:L.23, B:A.28, B:V.32, B:P.81, B:V.82, B:I.84, A:P.81, A:V.82 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: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

Pol polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pol polyprotein

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