SMTL ID : 2j9k.1

Atomic-resolution Crystal Structure of Chemically-Synthesized HIV-1 Protease Complexed with Inhibitor MVT-101

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

1 x 2NC: N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide(Non-covalent)

2NC.1: 28 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, T.80, P.81, V.82, I.84 Chain B: R.8, L.23, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, V.82, I.84 29 PLIP interactions: 15 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:L.23, A:A.28, A:P.81, A:V.82, A:I.84, B:L.23, B:A.28, B:D.30, B:I.47, B:I.50, B:I.50, B:V.82 Hydrogen bonds: A:G.27, A:D.29, A:D.29, A:D.29, A:D.30, A:D.30, A:D.30, A:G.48, A:G.48, B:G.27, B:D.29, B:G.48, B:G.48 Water bridges: A:I.50, B:R.8, B:G.48, B:I.50

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

SO4.2: 2 residues within 4Å: Chain A: P.1, H.69 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.69 SO4.3: 3 residues within 4Å: Chain A: G.73, T.74, N.88 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.74, A:T.74, A:N.88 Water bridges: A:Q.61, A:N.88, A:Q.92 SO4.8: 4 residues within 4Å: Chain B: R.14, G.16, G.17, P.63 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.16, B:G.17 Water bridges: B:R.14, B:R.14, B:R.14 Salt bridges: B:R.14 SO4.9: 3 residues within 4Å: Chain B: P.1 Ligands: GOL.6, SO4.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.1 SO4.10: 4 residues within 4Å: Chain B: P.1, H.69 Ligands: GOL.6, SO4.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.1 Salt bridges: B:H.69

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

ACT.4: 2 residues within 4Å: Chain A: K.7, R.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.7 ACT.5: 4 residues within 4Å: Chain A: W.42, K.55, V.56, R.57 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.55 Salt bridges: A:R.57 ACT.11: 5 residues within 4Å: Chain B: I.72, G.73, T.74, N.88, Q.92 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:N.88 Hydrogen bonds: B:T.74, B:T.74, B:T.74, B:Q.92 Water bridges: B:Q.61, B:Q.61 ACT.12: 3 residues within 4Å: Chain A: R.87 Chain B: K.7, R.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.8 Hydrogen bonds: B:R.8 Water bridges: B:K.7, B:R.8 Salt bridges: B:K.7, B:R.8 ACT.13: 2 residues within 4Å: Chain B: R.14, K.70 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.70

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: F.99 Chain B: P.1, H.69 Ligands: SO4.9, SO4.10 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.99, B:H.69 Water bridges: A:F.99 GOL.7: 2 residues within 4Å: Chain A: V.11, T.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.12, A:T.12 Water bridges: A:T.12, A:T.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, E.C.B. et al., Insights from Atomic-Resolution X-Ray Structures of Chemically Synthesized HIV-1 Protease in Complex with Inhibitors. J.Mol.Biol. (2007)

Release Date

2007-08-28

Peptides

PROTEASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTEASE

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