SMTL ID : 9dr0.1

Hare calicivirus protruding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 16 residues within 4Å: Chain A: N.140, G.141, T.142, V.143, Q.144, G.176, V.177, A.178 Chain B: N.140, G.141, T.142, V.143, Q.144, G.176, V.177, A.178 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.144, A:A.178, B:G.141, B:Q.144, B:A.178 EDO.2: 6 residues within 4Å: Chain A: P.138, Y.139, N.140, G.141, I.179, Q.181 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.138, A:N.140, A:N.140, A:G.141 Water bridges: A:Q.181 EDO.3: 10 residues within 4Å: Chain A: R.26, N.45, R.46, F.62, S.63, G.105, F.106, P.107, W.124, S.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.46, A:R.46, A:S.192 EDO.6: 7 residues within 4Å: Chain B: P.279, G.280, Q.281, N.299, V.300, D.301, N.331 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.280, B:D.301, B:N.331 Water bridges: B:Q.281, B:N.299, B:N.299, B:V.300, B:N.331 EDO.7: 5 residues within 4Å: Chain B: N.49, L.50, N.51, V.300, D.301 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.50, B:N.51 Water bridges: B:N.51, B:D.301 EDO.8: 4 residues within 4Å: Chain B: N.202, A.203, N.251, G.252 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.202, B:A.203, B:N.251

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

ACY.4: 6 residues within 4Å: Chain A: G.113, F.114, N.156, S.157, I.158, K.172 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.114 Hydrogen bonds: A:P.155, A:I.158 Salt bridges: A:K.172 ACY.5: 7 residues within 4Å: Chain B: G.113, F.114, P.155, N.156, S.157, I.158, K.172 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.158 Hydrogen bonds: B:F.114 Water bridges: B:K.172, B:K.172 Salt bridges: B:K.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hansman, G.S. et al., Structural analysis of a non-pathogenic hare calicivirus capsid bound to a histo-blood group antigen co-factor. J.Virol. (2024)

Release Date

2024-10-30

Peptides

Hare calicivirus protruding domain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hare calicivirus protruding domain