SMTL ID : 4imq.1

Structural Basis of Substrate Specificity and Protease Inhibition in Norwalk Virus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x PHQ- LEU- PHE- 1HD: PEPTIDE INHIBITOR, syc8(Non-covalent)

PHQ-LEU-PHE-1HD.1: 20 residues within 4Å: Chain A: H.32, E.56, I.111, Q.112, V.116, T.136, I.137, P.138, C.141, H.159, A.160, A.161, A.162, T.163, K.164 Chain B: G.178, E.179, A.181, L.182, E.183 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.56, A:I.111, A:Q.112, A:Q.112, A:V.116, A:A.162, A:T.163, A:K.164, B:E.183, B:E.183 Hydrogen bonds: A:Q.112, A:A.160, A:A.162, A:A.162, B:E.183 Water bridges: A:S.16, A:C.141 PHQ-LEU-PHE-1HD.5: 20 residues within 4Å: Chain A: G.178, E.179, A.181, L.182, E.183 Chain B: H.32, E.56, I.111, Q.112, V.116, T.136, I.137, P.138, C.141, H.159, A.160, A.161, A.162, T.163, K.164 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.56, B:I.111, B:Q.112, B:Q.112, B:V.116, B:A.162, B:T.163, B:K.164, A:E.183, A:E.183 Hydrogen bonds: B:Q.112, B:T.136, B:A.160, B:A.162, B:A.162, A:E.183, A:E.183 Water bridges: B:S.16, B:C.141

4 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.2: 4 residues within 4Å: Chain A: P.4, T.6, L.7, R.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.7 SCN.4: 6 residues within 4Å: Chain A: H.52, Q.53, A.54, F.57, Q.174, A.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.175 SCN.6: 4 residues within 4Å: Chain B: P.4, T.6, L.7, R.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.7 SCN.8: 6 residues within 4Å: Chain B: H.52, Q.53, A.54, F.57, Q.174, A.175 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.175

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

NA.3: 6 residues within 4Å: Chain A: L.123, G.135, T.136, A.162, G.166, V.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.136, A:T.136 NA.7: 6 residues within 4Å: Chain B: L.123, G.135, T.136, A.162, G.166, V.169 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.136, B:T.136 Water bridges: B:T.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muhaxhiri, Z. et al., Structural basis of substrate specificity and protease inhibition in norwalk virus. J.Virol. (2013)

Release Date

2013-02-20

Peptides

3C-like protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like protease