SMTL ID : 2aoe.1

crystal structure analysis of HIV-1 protease mutant V82A with a substrate analog CA-P2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 1 residues within 4Å: Chain A: D.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.60, A:D.60 Water bridges: A:R.41

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

CL.2: 3 residues within 4Å: Chain A: G.73, T.74, N.88 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP

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

DMS.3: 2 residues within 4Å: Chain A: K.45, M.46 No protein-ligand interaction detected (PLIP)

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 6 residues within 4Å: Chain A: T.12, I.13, L.19, E.65, A.67, G.68 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.12 Hydrogen bonds: A:T.12, A:A.67, A:G.68

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: Q.92, I.93, G.94 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.92 GOL.6: 4 residues within 4Å: Chain A: E.21, E.34, A.82, N.83 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.21, A:N.83 Water bridges: A:E.34, A:E.34, A:N.83 GOL.10: 6 residues within 4Å: Chain B: E.35, W.42, K.55, R.57, V.77, G.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.57, B:V.77

1 x 0Q4: N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucinamide(Non-covalent)

0Q4.7: 29 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.50, F.53, P.81, I.84 Chain B: R.8, L.23, D.25, G.27, A.28, D.29, D.30, M.46, I.47, G.48, G.49, I.50, P.81, A.82, I.84 26 PLIP interactions: 16 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:L.23, B:A.28, B:I.47, B:I.50, B:P.81, B:A.82, B:I.84, A:L.23, A:A.28, A:V.32, A:I.50, A:P.81 Hydrogen bonds: B:G.27, B:D.29, B:D.29, B:D.30, B:M.46, B:G.48, B:G.48, A:G.27, A:D.29, A:G.48 Water bridges: B:I.50, B:I.50, A:G.48, A:G.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tie, Y. et al., Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs. Febs J. (2005)

Release Date

2006-01-17

Peptides

POL POLYPROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

POL POLYPROTEIN

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