SMTL ID : 6p4k.3 (3 other biounits)

mouse norovirus complexed with TCA

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-18-mer

Ligands

36 x TCH: TAUROCHOLIC ACID(Covalent)(Non-covalent)

TCH.1: 6 residues within 4Å: Chain A: I.294, Q.296, G.298, R.374, R.376, V.378 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.294, A:R.374, A:R.376 Hydrogen bonds: A:R.374, A:R.374 Salt bridges: A:R.376 TCH.2: 6 residues within 4Å: Chain A: W.229, A.231, Y.234, Y.419, M.420, R.421 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.234, A:Y.234, A:Y.419 Hydrogen bonds: A:Y.419, A:Y.419 Salt bridges: A:R.421 TCH.3: 13 residues within 4Å: Chain B: D.297, G.298, Q.324, R.374, V.375, R.376, V.378 Chain D: W.229, Y.234, Y.419, M.420, R.421 Ligands: TCH.8 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.234, D:Y.234, D:Y.419 Salt bridges: D:R.421, B:R.376 TCH.4: 13 residues within 4Å: Chain B: W.229, P.230, A.231, Y.234, Y.419, M.420, R.421 Chain D: Q.296, G.298, R.374, R.376, V.378 Ligands: TCH.7 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:R.374, D:R.376, B:Y.234, B:Y.234, B:Y.419, B:Y.419 Salt bridges: D:R.376, B:R.421 Hydrogen bonds: B:R.421 TCH.5: 11 residues within 4Å: Chain C: G.298, Q.324, R.374, R.376 Chain I: W.229, A.231, Y.234, Y.419, M.420, R.421 Ligands: TCH.18 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain I Hydrophobic interactions: C:Q.324, I:Y.234, I:Y.419, I:Y.419 Hydrogen bonds: C:R.374, I:Y.419 Salt bridges: C:R.376, I:R.421 TCH.6: 8 residues within 4Å: Chain C: Y.234, Y.419, R.421 Chain I: Q.324, R.374, R.376, V.378 Ligands: TCH.17 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain I Hydrophobic interactions: C:Y.234, C:Y.419, C:Y.419, I:Q.324 Hydrogen bonds: C:R.421, I:R.376 Salt bridges: C:R.421, I:R.376 TCH.7: 13 residues within 4Å: Chain B: W.229, P.230, A.231, Y.234, Y.419, R.421 Chain D: I.294, Q.296, G.298, R.374, R.376, V.378 Ligands: TCH.4 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:I.294, D:R.374, D:R.376, B:Y.419, B:Y.419 Hydrogen bonds: D:R.374, B:Y.234, B:R.421 Salt bridges: D:R.376, B:R.421 TCH.8: 15 residues within 4Å: Chain B: I.294, Q.296, D.297, G.298, Q.324, R.374, V.375, R.376 Chain D: W.229, A.231, Y.234, Y.419, M.420, R.421 Ligands: TCH.3 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:Y.234, D:Y.234, D:Y.419, B:I.294 Hydrogen bonds: D:Y.419, D:Y.419 Salt bridges: D:R.421, B:R.376 TCH.9: 7 residues within 4Å: Chain E: D.297, G.298, Q.324, R.374, V.375, R.376, V.378 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.374 Salt bridges: E:R.376 TCH.10: 7 residues within 4Å: Chain E: W.229, P.230, A.231, Y.234, Y.419, M.420, R.421 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:Y.234, E:Y.234, E:Y.419, E:Y.419 Hydrogen bonds: E:W.229 Salt bridges: E:R.421 TCH.11: 11 residues within 4Å: Chain F: G.298, Q.324, R.374, R.376 Chain O: W.229, A.231, Y.234, Y.419, M.420, R.421 Ligands: TCH.30 8 PLIP interactions: 5 interactions with chain O, 3 interactions with chain F Hydrophobic interactions: O:Y.234, O:Y.419, O:Y.419, F:Q.324 Hydrogen bonds: O:Y.419, F:R.374 Salt bridges: O:R.421, F:R.376 TCH.12: 8 residues within 4Å: Chain F: Y.234, Y.419, R.421 Chain O: Q.324, R.374, R.376, V.378 Ligands: TCH.29 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain O Hydrophobic interactions: F:Y.234, F:Y.419, F:Y.419, O:Q.324 Hydrogen bonds: F:R.421, O:R.376 Salt bridges: F:R.421, O:R.376 TCH.13: 13 residues within 4Å: Chain G: I.294, Q.296, G.298, R.374, R.376, V.378 Chain K: W.229, P.230, A.231, Y.234, Y.419, R.421 Ligands: TCH.22 11 PLIP interactions: 6 interactions with chain G, 5 interactions with chain K Hydrophobic interactions: G:I.294, G:R.374, G:R.376, K:Y.419, K:Y.419 Hydrogen bonds: G:R.374, G:R.374, K:Y.234, K:R.421 Salt bridges: G:R.376, K:R.421 TCH.14: 15 residues within 4Å: Chain G: W.229, A.231, Y.234, Y.419, M.420, R.421 Chain K: I.294, Q.296, D.297, G.298, Q.324, R.374, V.375, R.376 Ligands: TCH.21 8 PLIP interactions: 6 interactions with chain G, 2 interactions with chain K Hydrophobic interactions: G:Y.234, G:Y.234, G:Y.419, K:I.294 Hydrogen bonds: G:Y.419, G:Y.419 Salt bridges: G:R.421, K:R.376 TCH.15: 7 residues within 4Å: Chain H: D.297, G.298, Q.324, R.374, V.375, R.376, V.378 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.374 Salt bridges: H:R.376 TCH.16: 7 residues within 4Å: Chain H: W.229, P.230, A.231, Y.234, Y.419, M.420, R.421 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:Y.234, H:Y.234, H:Y.419, H:Y.419 Hydrogen bonds: H:W.229 Salt bridges: H:R.421 TCH.17: 11 residues within 4Å: Chain C: W.229, A.231, Y.234, Y.419, M.420, R.421 Chain I: G.298, Q.324, R.374, R.376 Ligands: TCH.6 8 PLIP interactions: 3 interactions with chain I, 5 interactions with chain C Hydrophobic interactions: I:Q.324, C:Y.234, C:Y.419, C:Y.419 Hydrogen bonds: I:R.374, C:Y.419 Salt bridges: I:R.376, C:R.421 TCH.18: 8 residues within 4Å: Chain C: Q.324, R.374, R.376, V.378 Chain I: Y.234, Y.419, R.421 Ligands: TCH.5 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain I Hydrophobic interactions: C:Q.324, I:Y.234, I:Y.419, I:Y.419 Hydrogen bonds: C:R.376, I:R.421 Salt bridges: C:R.376, I:R.421 TCH.19: 6 residues within 4Å: Chain J: I.294, Q.296, G.298, R.374, R.376, V.378 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:I.294, J:R.374, J:R.376 Hydrogen bonds: J:R.374, J:R.374 Salt bridges: J:R.376 TCH.20: 6 residues within 4Å: Chain J: W.229, A.231, Y.234, Y.419, M.420, R.421 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:Y.234, J:Y.234, J:Y.419 Hydrogen bonds: J:Y.419, J:Y.419 Salt bridges: J:R.421 TCH.21: 13 residues within 4Å: Chain G: W.229, Y.234, Y.419, M.420, R.421 Chain K: D.297, G.298, Q.324, R.374, V.375, R.376, V.378 Ligands: TCH.14 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain K Hydrophobic interactions: G:Y.234, G:Y.234, G:Y.419 Salt bridges: G:R.421, K:R.376 Hydrogen bonds: K:R.374 TCH.22: 13 residues within 4Å: Chain G: Q.296, G.298, R.374, R.376, V.378 Chain K: W.229, P.230, A.231, Y.234, Y.419, M.420, R.421 Ligands: TCH.13 9 PLIP interactions: 3 interactions with chain G, 6 interactions with chain K Hydrophobic interactions: G:R.374, G:R.376, K:Y.234, K:Y.234, K:Y.419, K:Y.419 Salt bridges: G:R.376, K:R.421 Hydrogen bonds: K:W.229 TCH.23: 11 residues within 4Å: Chain L: G.298, Q.324, R.374, R.376 Chain R: W.229, A.231, Y.234, Y.419, M.420, R.421 Ligands: TCH.36 8 PLIP interactions: 3 interactions with chain L, 5 interactions with chain R Hydrophobic interactions: L:Q.324, R:Y.234, R:Y.419, R:Y.419 Hydrogen bonds: L:R.374, R:Y.419 Salt bridges: L:R.376, R:R.421 TCH.24: 8 residues within 4Å: Chain L: Y.234, Y.419, R.421 Chain R: Q.324, R.374, R.376, V.378 Ligands: TCH.35 8 PLIP interactions: 5 interactions with chain L, 3 interactions with chain R Hydrophobic interactions: L:Y.234, L:Y.419, L:Y.419, R:Q.324 Hydrogen bonds: L:R.421, R:R.376 Salt bridges: L:R.421, R:R.376 TCH.25: 6 residues within 4Å: Chain M: I.294, Q.296, G.298, R.374, R.376, V.378 6 PLIP interactions: 6 interactions with chain M Hydrophobic interactions: M:I.294, M:R.374, M:R.376 Hydrogen bonds: M:R.374, M:R.374 Salt bridges: M:R.376 TCH.26: 6 residues within 4Å: Chain M: W.229, A.231, Y.234, Y.419, M.420, R.421 6 PLIP interactions: 6 interactions with chain M Hydrophobic interactions: M:Y.234, M:Y.234, M:Y.419 Hydrogen bonds: M:Y.419, M:Y.419 Salt bridges: M:R.421 TCH.27: 13 residues within 4Å: Chain N: D.297, G.298, Q.324, R.374, V.375, R.376, V.378 Chain P: W.229, Y.234, Y.419, M.420, R.421 Ligands: TCH.32 6 PLIP interactions: 2 interactions with chain N, 4 interactions with chain P Hydrogen bonds: N:R.374 Salt bridges: N:R.376, P:R.421 Hydrophobic interactions: P:Y.234, P:Y.234, P:Y.419 TCH.28: 13 residues within 4Å: Chain N: W.229, P.230, A.231, Y.234, Y.419, M.420, R.421 Chain P: Q.296, G.298, R.374, R.376, V.378 Ligands: TCH.31 9 PLIP interactions: 6 interactions with chain N, 3 interactions with chain P Hydrophobic interactions: N:Y.234, N:Y.234, N:Y.419, N:Y.419, P:R.374, P:R.376 Hydrogen bonds: N:W.229 Salt bridges: N:R.421, P:R.376 TCH.29: 11 residues within 4Å: Chain F: W.229, A.231, Y.234, Y.419, M.420, R.421 Chain O: G.298, Q.324, R.374, R.376 Ligands: TCH.12 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain O Hydrophobic interactions: F:Y.234, F:Y.419, F:Y.419, O:Q.324 Hydrogen bonds: F:Y.419, O:R.374 Salt bridges: F:R.421, O:R.376 TCH.30: 8 residues within 4Å: Chain F: Q.324, R.374, R.376, V.378 Chain O: Y.234, Y.419, R.421 Ligands: TCH.11 8 PLIP interactions: 3 interactions with chain F, 5 interactions with chain O Hydrophobic interactions: F:Q.324, O:Y.234, O:Y.419, O:Y.419 Hydrogen bonds: F:R.376, O:R.421 Salt bridges: F:R.376, O:R.421 TCH.31: 13 residues within 4Å: Chain N: W.229, P.230, A.231, Y.234, Y.419, R.421 Chain P: I.294, Q.296, G.298, R.374, R.376, V.378 Ligands: TCH.28 11 PLIP interactions: 6 interactions with chain P, 5 interactions with chain N Hydrophobic interactions: P:I.294, P:R.374, P:R.376, N:Y.419, N:Y.419 Hydrogen bonds: P:R.374, P:R.374, N:Y.234, N:R.421 Salt bridges: P:R.376, N:R.421 TCH.32: 15 residues within 4Å: Chain N: I.294, Q.296, D.297, G.298, Q.324, R.374, V.375, R.376 Chain P: W.229, A.231, Y.234, Y.419, M.420, R.421 Ligands: TCH.27 8 PLIP interactions: 2 interactions with chain N, 6 interactions with chain P Hydrophobic interactions: N:I.294, P:Y.234, P:Y.234, P:Y.419 Salt bridges: N:R.376, P:R.421 Hydrogen bonds: P:Y.419, P:Y.419 TCH.33: 7 residues within 4Å: Chain Q: D.297, G.298, Q.324, R.374, V.375, R.376, V.378 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:R.374 Salt bridges: Q:R.376 TCH.34: 7 residues within 4Å: Chain Q: W.229, P.230, A.231, Y.234, Y.419, M.420, R.421 6 PLIP interactions: 6 interactions with chain Q Hydrophobic interactions: Q:Y.234, Q:Y.234, Q:Y.419, Q:Y.419 Hydrogen bonds: Q:W.229 Salt bridges: Q:R.421 TCH.35: 11 residues within 4Å: Chain L: W.229, A.231, Y.234, Y.419, M.420, R.421 Chain R: G.298, Q.324, R.374, R.376 Ligands: TCH.24 8 PLIP interactions: 5 interactions with chain L, 3 interactions with chain R Hydrophobic interactions: L:Y.234, L:Y.419, L:Y.419, R:Q.324 Hydrogen bonds: L:Y.419, R:R.374 Salt bridges: L:R.421, R:R.376 TCH.36: 8 residues within 4Å: Chain L: Q.324, R.374, R.376, V.378 Chain R: Y.234, Y.419, R.421 Ligands: TCH.23 8 PLIP interactions: 3 interactions with chain L, 5 interactions with chain R Hydrophobic interactions: L:Q.324, R:Y.234, R:Y.419, R:Y.419 Hydrogen bonds: L:R.376, R:R.421 Salt bridges: L:R.376, R:R.421

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sherman, M.B. et al., Bile Salts Alter the Mouse Norovirus Capsid Conformation: Possible Implications for Cell Attachment and Immune Evasion. J.Virol. (2019)

Release Date

2019-08-07

Peptides

Capsid protein: ABCDEFGHIJKLMNOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

M
A

N
B

O
C

P
A

Q
B

R
C

Capsid protein

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