SMTL ID : 7whp.1

Pentameric turret of Bombyx mori cytoplasmic polyhedrosis virus after spike detaches.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 16 residues within 4Å: Chain A: N.526, S.528, L.561, G.562, A.563, E.564, E.566, D.589, R.590, R.599, V.600, D.616, I.617, N.618, Y.620, E.631 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.526, A:S.528, A:G.562, A:A.563, A:E.564, A:E.564, A:E.564, A:E.566, A:D.589, A:R.590, A:R.590, A:R.599, A:V.600, A:V.600 Salt bridges: A:E.564 SAM.2: 18 residues within 4Å: Chain A: K.838, Y.842, I.861, G.862, G.863, R.864, D.868, I.881, D.882, P.883, F.904, F.906, I.922, A.923, V.924, E.928, P.929, Y.992 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.862, A:R.864, A:F.904, A:F.904 Salt bridges: A:K.838 SAM.4: 17 residues within 4Å: Chain B: N.526, S.528, L.561, G.562, A.563, E.564, E.566, G.588, D.589, R.590, R.599, V.600, D.616, I.617, N.618, Y.620, E.631 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.526, B:S.528, B:G.562, B:A.563, B:E.564, B:E.564, B:D.589, B:R.590, B:R.599, B:V.600, B:V.600 SAM.5: 19 residues within 4Å: Chain B: K.838, Y.842, G.862, G.863, R.864, D.868, I.881, D.882, P.883, A.884, P.903, F.904, F.906, I.922, A.923, V.924, E.928, P.929, Y.992 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.842, B:G.862, B:R.864, B:R.864, B:F.904, B:F.904, B:P.929 Salt bridges: B:K.838

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 5 residues within 4Å: Chain A: Y.268, R.271, D.302, Y.305, Y.316 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.268, A:R.271, A:Y.316, A:Y.316 Salt bridges: A:R.271 pi-Stacking: A:Y.305, A:Y.305 pi-Cation interactions: A:R.271 ATP.6: 5 residues within 4Å: Chain B: Y.268, R.271, D.302, Y.305, Y.320 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.268, B:R.271, B:Y.320 Salt bridges: B:R.271 pi-Stacking: B:Y.305 pi-Cation interactions: B:R.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Multiple conformations of trimeric spikes visualized on a non-enveloped virus. Nat Commun (2022)

Release Date

2022-02-02

Peptides

Structural protein VP3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Structural protein VP3

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