SMTL ID : 5kon.1

Protruding domain of GII.4 human norovirus isolate 08-14

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: F.30, F.37, Q.182, W.183, F.213, R.215, D.230 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.183, A:R.215, A:D.230, A:D.230 Water bridges: A:P.33, A:Q.182 EDO.2: 2 residues within 4Å: Chain A: D.69, N.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.158 EDO.3: 5 residues within 4Å: Chain A: L.266, H.285, L.287, V.288, M.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.285, A:V.288 EDO.4: 6 residues within 4Å: Chain A: N.259, T.262, R.264, V.265, L.266, P.290 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.259, A:T.262, A:T.262, A:R.264, A:R.264 EDO.5: 6 residues within 4Å: Chain A: L.52, L.53, G.54, T.56, I.97, L.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.56 Water bridges: A:G.54, A:G.54, A:E.96 EDO.6: 3 residues within 4Å: Chain A: G.3, K.5, P.6 No protein-ligand interaction detected (PLIP) EDO.7: 5 residues within 4Å: Chain A: G.75, S.76, R.77, D.152 Ligands: MES.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.76, A:D.152 EDO.8: 7 residues within 4Å: Chain A: V.107, G.134, V.184, L.185, P.186, S.187, R.191 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.187, A:R.191 Water bridges: A:T.133, A:S.187, A:S.187, A:S.187 EDO.9: 9 residues within 4Å: Chain A: W.88, T.115, Q.116, T.117, N.160, T.161, K.162 Chain B: P.219, G.220 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Water bridges: B:T.217, B:G.220, B:G.220, A:W.88 Hydrogen bonds: A:T.115, A:T.115 EDO.10: 8 residues within 4Å: Chain A: T.65, F.66, R.67, L.83, A.84, S.85, Q.86, P.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.67 Water bridges: A:L.101 EDO.13: 5 residues within 4Å: Chain B: L.266, H.285, L.287, V.288, M.310 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.285, B:V.288 EDO.14: 7 residues within 4Å: Chain B: F.30, F.37, Q.182, W.183, F.213, R.215, D.230 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.183, B:R.215, B:D.230 Water bridges: B:Q.182, B:Q.284 EDO.15: 6 residues within 4Å: Chain B: L.52, L.53, G.54, T.56, I.97, L.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.56 Water bridges: B:L.52, B:G.54 EDO.16: 9 residues within 4Å: Chain A: P.219, G.220 Chain B: W.88, T.115, Q.116, T.117, N.160, T.161, K.162 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:M.218, A:G.220, B:T.117 Hydrogen bonds: B:T.115, B:T.115 EDO.17: 7 residues within 4Å: Chain A: Q.239, Q.243 Chain B: P.10, L.12, E.236, Q.239, Y.240 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.239, A:Q.243 Water bridges: A:Q.239

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.11: 6 residues within 4Å: Chain A: R.77, D.150, T.151, D.152, H.153 Ligands: EDO.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.151, A:D.152 Salt bridges: A:R.77, A:D.152, A:H.153 MES.12: 7 residues within 4Å: Chain A: S.85, Q.86, Y.91, E.95, I.97, P.100, L.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.86, A:L.101 Salt bridges: A:E.95 MES.18: 7 residues within 4Å: Chain B: S.85, Q.86, Y.91, E.95, I.97, P.100, L.101 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.86, B:L.101 Water bridges: B:S.85, B:N.87, B:E.95, B:E.95 Salt bridges: B:E.95

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Singh, B.K. et al., Four decades of structural evolution of GII.4 norovirus. To be published

Release Date

2017-05-24

Peptides

VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VP1