SMTL ID : 3slz.1

The crystal structure of XMRV protease complexed with TL-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

1 x 3TL: benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate(Non-covalent)

3TL.1: 32 residues within 4Å: Chain A: L.37, D.39, G.41, A.42, Q.43, A.59, W.60, V.61, Q.62, G.63, A.64, W.72, C.95, P.96, Y.97, L.99 Chain B: D.39, G.41, A.42, Q.43, H.44, A.59, W.60, V.61, Q.62, G.63, A.64, W.72, P.96, Y.97, L.99 Ligands: FMT.7 34 PLIP interactions: 18 interactions with chain B, 16 interactions with chain A Hydrophobic interactions: B:Q.43, B:H.44, B:A.59, B:V.61, B:A.64, B:W.72, B:W.72, B:P.96, B:Y.97, A:L.37, A:A.59, A:V.61, A:Q.62, A:A.64, A:W.72, A:P.96, A:Y.97 Hydrogen bonds: B:D.39, B:G.41, B:G.41, B:Q.43, B:Q.43, B:Q.62, B:Q.62, A:G.41, A:Q.43, A:Q.43, A:Q.62, A:Q.62 Water bridges: B:A.64, B:R.102, A:Q.62, A:A.64, A:R.102

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 4 residues within 4Å: Chain A: H.44, W.72, H.87, S.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.88 Water bridges: A:T.86, A:H.87 FMT.3: 4 residues within 4Å: Chain A: T.73, T.74, D.75, S.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.75, A:D.75, A:S.88 FMT.4: 3 residues within 4Å: Chain B: H.44, H.87, S.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.44, B:S.88 FMT.5: 4 residues within 4Å: Chain B: G.116, S.117, G.118 Ligands: NA.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.118 FMT.6: 4 residues within 4Å: Chain B: L.47, T.48, Q.49, P.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.48, B:Q.49 Water bridges: B:T.48 FMT.7: 3 residues within 4Å: Chain B: Q.43, W.60 Ligands: 3TL.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.43 Water bridges: B:Q.43, B:W.60

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

NA.8: 4 residues within 4Å: Chain B: F.114, G.116, G.118 Ligands: FMT.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.114 Water bridges: B:G.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., Structural and biochemical characterization of the inhibitor complexes of xenotropic murine leukemia virus-related virus protease. Febs J. (2011)

Release Date

2011-10-12

Peptides

gag-pro-pol polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

gag-pro-pol polyprotein

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