SMTL ID : 4rox.1

Crystal Structure of P Domain of Hawaii Norovirus (GII.1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: L.52, L.53, G.54, T.56, V.99, L.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.56 Water bridges: A:G.54 EDO.2: 7 residues within 4Å: Chain A: E.231, Q.234, H.235 Chain B: Q.234, Q.238 Ligands: EDO.3, EDO.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.234 Hydrogen bonds: A:H.235 EDO.3: 8 residues within 4Å: Chain A: H.235, Q.238, E.239 Chain B: H.235, Q.238, E.239 Ligands: EDO.2, EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.239 EDO.4: 5 residues within 4Å: Chain A: E.28, Y.30, R.210, H.212, P.281 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.28, A:R.210 EDO.5: 6 residues within 4Å: Chain B: P.95, T.96, E.97, D.98, K.142, N.192 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.142, B:K.142, B:N.192 EDO.6: 7 residues within 4Å: Chain A: Q.234, Q.238 Chain B: E.231, Q.234, H.235 Ligands: EDO.2, EDO.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.234, A:Q.234, A:Q.238 Hydrogen bonds: B:H.235 EDO.7: 6 residues within 4Å: Chain B: L.52, L.53, G.54, T.56, V.99, L.103 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.56 Water bridges: B:G.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, B.K. et al., Structural Constraints on Human Norovirus Binding to Histo-Blood Group Antigens. mSphere (2016)

Release Date

2016-05-25

Peptides

Capsid protein VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Capsid protein VP1

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