SMTL ID : 2fgu.1

X-ray crystal structure of HIV-1 Protease T80S variant in complex with the inhibitor saquinavir used to explore the role of invariant Thr80 in HIV-1 protease structure, function, and viral infectivity.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: R.14, G.16, G.17, P.63 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.16, A:G.17 Water bridges: A:R.14, A:R.14 Salt bridges: A:R.14 PO4.2: 4 residues within 4Å: Chain A: G.73, T.74, N.88, Q.92 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.74, A:T.74, A:T.74, A:N.88, A:Q.92 Water bridges: A:Q.61, A:G.73, A:N.88 PO4.3: 2 residues within 4Å: Chain A: P.1 Chain B: F.99 No protein-ligand interaction detected (PLIP) PO4.9: 2 residues within 4Å: Chain B: M.36, N.37 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.37 Water bridges: B:M.36, B:N.37 PO4.10: 3 residues within 4Å: Chain B: K.20, E.21, N.83 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.21, B:N.83 Water bridges: B:E.34 Salt bridges: B:K.20

1 x QNC: quinoline-2-carboxylic acid(Non-covalent)

QNC.4: 8 residues within 4Å: Chain A: G.27, A.28, D.29, G.48 Chain B: R.8, P.81 Ligands: ASN.5, HPH.6 5 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: N.5, A:D.29 Hydrophobic interactions: B:P.81, B:P.81 Water bridges: A:G.48

1 x ASN: ASPARAGINE(Non-covalent)

ASN.5: 9 residues within 4Å: Chain A: A.28, D.29, D.30, I.47, G.48, G.49 Chain B: I.50 Ligands: QNC.4, HPH.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.29, A:D.30, A:D.30, A:D.30, A:G.48 Water bridges: A:G.48, A:I.50

1 x HPH: (2S)-2-amino-3-phenylpropane-1,1-diol(Non-covalent)

HPH.6: 12 residues within 4Å: Chain A: D.25, G.27, A.28, G.49, I.50 Chain B: L.23, D.25, P.81, I.84 Ligands: QNC.4, ASN.5, DIQ.7 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.50, B:L.23, B:P.81, B:I.84 Hydrogen bonds: A:G.27, A:G.27, A:G.27

1 x DIQ: 2-METHYL-DECAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID(Non-covalent)

DIQ.7: 12 residues within 4Å: Chain A: L.23, D.25, S.80, P.81, V.82, I.84 Chain B: D.25, G.27, G.49, I.50 Ligands: HPH.6, NTB.8 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.81, A:V.82, A:I.84, B:I.50 Salt bridges: A:D.25, B:D.25 Water bridges: B:I.50, B:I.50

1 x NTB: TERTIARY-BUTYLAMINE(Non-covalent)

NTB.8: 6 residues within 4Å: Chain A: I.50 Chain B: A.28, D.30, I.47, G.48 Ligands: DIQ.7 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.50, B:D.30, B:I.47 Water bridges: B:G.27, B:D.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Foulkes, J.E. et al., Role of invariant Thr80 in human immunodeficiency virus type 1 protease structure, function, and viral infectivity. J.Virol. (2006)

Release Date

2006-11-07

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease