SMTL ID : 1nh0.1

1.03 A structure of HIV-1 protease: inhibitor binding inside and outside the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.03 Å

Oligo State

homo-dimer

Ligands

2 x KI2- PHE- GLU- GLU- NH2: peptidomimetic inhibitor KI2-PHE-GLU-GLU-NH2(Non-covalent)

KI2-PHE-GLU-GLU-NH2.1: 25 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, P.81, V.82 Chain B: R.8, L.23, D.25, G.27, A.28, D.30, V.32, I.47, G.48, G.49, I.50, L.76, P.81, V.82, I.84 31 PLIP interactions: 13 interactions with chain A, 18 interactions with chain B Hydrophobic interactions: A:A.28, A:I.47, A:P.81, A:V.82, B:L.23, B:D.30, B:V.32, B:I.47, B:I.47, B:I.47, B:I.50, B:L.76, B:P.81, B:P.81, B:V.82, B:I.84 Hydrogen bonds: A:G.27, A:D.29, A:D.30, A:G.48, A:G.48, A:I.50, B:G.27, B:G.27 Water bridges: A:D.29, A:D.29, A:D.30, B:R.8, B:R.8, B:I.50 Salt bridges: B:R.8 KI2-PHE-GLU-GLU-NH2.2: 5 residues within 4Å: Chain A: T.4, W.6 Chain B: Q.92, I.93, G.94 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.6 Hydrogen bonds: A:T.4

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

SO4.3: 3 residues within 4Å: Chain A: W.42, P.44, R.57 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.56 Salt bridges: A:R.57 SO4.5: 1 residues within 4Å: Chain B: R.41 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.41, B:R.41 Salt bridges: B:R.41

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.4: 4 residues within 4Å: Chain A: P.1, V.11, T.12, C.67 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.12 BME.6: 3 residues within 4Å: Chain B: V.11, T.12, C.67 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brynda, J. et al., A Phenylnorstatine Inhibitor Binding to HIV-1 Protease: Geometry, Protonation, and Subsite-Pocket Interactions Analyzed at Atomic Resolution. J.Med.Chem. (2004)

Release Date

2004-04-13

Peptides

PROTEASE RETROPEPSIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTEASE RETROPEPSIN

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