SMTL ID : 3ndx.1

HIV-1 Protease Saquinavir:Ritonavir 1:50 complex structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.03 Å

Oligo State

homo-dimer

Ligands

1 x RIT: RITONAVIR(Non-covalent)

RIT.1: 23 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, G.48, G.49, I.50, P.81, V.82, I.84 Chain B: R.8, D.25, G.27, A.28, D.29, D.30, G.48, G.49, I.50, V.82, I.84 Ligands: GOL.3 20 PLIP interactions: 8 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:I.50, A:P.81, A:P.81, A:V.82, A:I.84, B:A.28, B:I.50, B:I.50, B:V.82, B:I.84 Hydrogen bonds: A:G.27, B:D.25, B:G.27, B:D.29, B:G.48 Water bridges: A:D.29, B:D.29, B:I.50, B:I.50 pi-Cation interactions: A:R.8

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

DMS.2: 1 residues within 4Å: Chain A: Q.92 No protein-ligand interaction detected (PLIP) DMS.7: 8 residues within 4Å: Chain B: K.14, I.15, G.16, G.17, I.63, I.64, E.65 Ligands: DMS.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.17 DMS.8: 2 residues within 4Å: Chain B: M.36, S.37 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.37 DMS.9: 1 residues within 4Å: Ligands: DMS.7 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: G.48, F.53 Chain B: P.81 Ligands: RIT.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.48 GOL.6: 3 residues within 4Å: Chain B: V.11, T.12, A.67 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.12, B:T.12, B:T.12

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

CL.4: 2 residues within 4Å: Chain A: K.7, R.8 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain B: P.1, H.69 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:F.99, B:H.69 Hydrogen bonds: B:P.1 Salt bridges: B:H.69 SO4.10: 2 residues within 4Å: Chain B: H.69, K.70 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.70 Water bridges: B:G.68, B:K.70 Salt bridges: B:H.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olajuyigbe, F.M. et al., Investigation of 2-Fold Disorder of Inhibitors and Relative Potency by Crystallizations of HIV-1 Protease in Ritonavir and Saquinavir Mixtures. Cryst.Growth Des. (2011)

Release Date

2011-07-20

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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