SMTL ID : 6h6m.1

CR10 murine norovirus protruding domain in complex with the CD300lf receptor and glycochenodeoxycholate (GCDCA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

hetero-4-2-mer

Ligands

4 x CHO: GLYCOCHENODEOXYCHOLIC ACID(Non-covalent)

CHO.1: 15 residues within 4Å: Chain A: W.18, P.19, A.20, Y.23, Y.208, M.209, R.210 Chain B: A.63, I.83, Q.85, G.87, Q.113, R.163, V.164, R.165 16 PLIP interactions: 7 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:A.63, B:I.83, B:Q.113, B:R.163, A:Y.23, A:Y.23, A:Y.208 Hydrogen bonds: B:R.163, A:Y.208, A:Y.208, A:R.210 Water bridges: B:R.165, A:R.210, A:R.210 Salt bridges: B:R.165, A:R.210 CHO.7: 15 residues within 4Å: Chain A: A.63, I.83, Q.85, G.87, Q.113, R.163, V.164, R.165 Chain B: W.18, P.19, A.20, Y.23, Y.208, M.209, R.210 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:I.83, A:Q.113, A:R.163, B:Y.23, B:Y.23, B:Y.23, B:Y.208 Water bridges: A:R.165, B:R.210, B:R.210 Salt bridges: A:R.165, B:R.210 Hydrogen bonds: B:Y.208, B:Y.208, B:R.210 CHO.13: 14 residues within 4Å: Chain C: W.18, A.20, Y.23, Y.208, M.209, R.210 Chain D: A.63, E.65, Q.85, G.87, Q.113, R.163, V.164, R.165 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.23, C:Y.23, C:Y.208 Hydrogen bonds: C:Y.208, C:Y.208, C:R.210, D:E.65 Water bridges: C:R.210, C:R.210, D:R.165 Salt bridges: C:R.210, D:R.165 CHO.18: 15 residues within 4Å: Chain C: A.63, I.83, Q.85, G.87, Q.113, R.163, V.164, R.165 Chain D: W.18, P.19, A.20, Y.23, Y.208, M.209, R.210 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.23, D:Y.208, D:Y.208, C:I.83, C:R.163 Hydrogen bonds: D:Y.208, D:Y.208, D:R.210 Water bridges: D:R.210, D:R.210, C:R.165 Salt bridges: D:R.210, C:R.165

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

EDO.2: 6 residues within 4Å: Chain A: L.31, D.176, R.206, A.221, I.222, D.223 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.176, A:R.204, A:R.206, A:D.223 EDO.3: 5 residues within 4Å: Chain A: P.35, Q.36, W.37, D.176, I.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.36, A:I.178 Water bridges: A:Q.36 EDO.4: 7 residues within 4Å: Chain A: Y.68, Q.113, T.114, E.115, V.160, R.163, V.164 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.68, A:E.115, A:E.115, A:V.160 EDO.5: 6 residues within 4Å: Chain A: P.53, V.54, S.55, W.58, L.99 Chain B: L.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.54, A:S.55 EDO.9: 8 residues within 4Å: Chain B: R.17, L.31, F.174, D.176, R.204, A.221, I.222, D.223 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.17, B:D.176, B:D.223 Water bridges: B:D.176 EDO.10: 4 residues within 4Å: Chain B: P.35, Q.36, W.37, D.176 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.36, B:Q.36 Water bridges: B:Q.36, B:I.178 EDO.11: 8 residues within 4Å: Chain B: Y.68, Q.113, T.114, E.115, V.160, G.162, R.163, V.164 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.68, B:E.115, B:E.115 EDO.12: 6 residues within 4Å: Chain A: L.12 Chain B: P.53, V.54, S.55, W.58, L.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.54, B:S.55 EDO.14: 5 residues within 4Å: Chain C: P.35, Q.36, W.37, D.176, I.178 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.36, C:Q.36, C:I.178 Water bridges: C:N.34, C:Q.36 EDO.15: 6 residues within 4Å: Chain C: F.174, D.176, R.206, A.221, I.222, D.223 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.176, C:R.206, C:D.223 Water bridges: C:D.176, C:D.176 EDO.16: 8 residues within 4Å: Chain C: Y.68, Q.113, T.114, E.115, V.160, G.162, R.163, V.164 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.68, C:Y.68, C:E.115 EDO.20: 5 residues within 4Å: Chain D: P.35, Q.36, W.37, D.176, I.178 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.36, D:I.178 Water bridges: D:Q.36, D:D.176, D:V.177 EDO.21: 7 residues within 4Å: Chain D: L.31, F.174, D.176, R.206, A.221, I.222, D.223 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.206, D:D.223 Water bridges: D:R.206 EDO.22: 5 residues within 4Å: Chain E: G.12, Q.13, G.16, S.17, L.80 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.13, E:S.17 EDO.24: 5 residues within 4Å: Chain F: G.12, Q.13, G.16, S.17, L.80 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.13, F:S.17

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

NA.6: 6 residues within 4Å: Chain A: N.137, V.138, D.139 Chain E: K.94, G.96, D.98 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.94, E:D.98 NA.8: 3 residues within 4Å: Chain B: Q.211, D.213, E.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.213 Water bridges: B:Q.211 NA.17: 5 residues within 4Å: Chain C: N.137, D.139 Chain F: K.94, G.96, D.98 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.94, F:K.94 NA.19: 3 residues within 4Å: Chain D: Q.211, D.213, E.220 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.213, D:E.220

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.23: 3 residues within 4Å: Chain E: K.32, E.49, T.50 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.32

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.25: 5 residues within 4Å: Chain F: K.32, E.49, T.50, D.51, T.93 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kilic, T. et al., Crystal structures of murine norovirus protruding domain with conjugated bile acid reveal a novel binding pocket. To Be Published

Release Date

2019-08-14

Peptides

Capsid protein: ABCD
CMRF35-like molecule 1: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Capsid protein

CMRF35-like molecule 1

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