SMTL ID : 6o3v.1 (1 other biounit)

Crystal structure for RVA-VP3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-tetramer

Ligands

4 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.1: 9 residues within 4Å: Chain A: S.570, S.573, H.574, R.577, Y.588, R.591, H.612, N.615, H.650 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.570, A:H.574, A:Y.588, A:H.612, A:H.612, A:H.612, A:N.615 Salt bridges: A:R.577, A:R.591 5GP.4: 12 residues within 4Å: Chain B: S.570, S.573, H.574, R.577, Y.588, R.591, S.608, S.610, G.611, H.612, N.615, E.654 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.570, B:S.573, B:Y.588, B:S.610, B:G.611, B:H.612, B:N.615, B:E.654, B:E.654, B:E.654 Salt bridges: B:H.574, B:R.577, B:R.591 5GP.7: 9 residues within 4Å: Chain C: S.570, S.573, H.574, R.577, Y.588, R.591, H.612, N.615, H.650 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.570, C:H.574, C:H.612, C:H.612, C:H.612, C:N.615 Salt bridges: C:R.577, C:R.591 5GP.10: 12 residues within 4Å: Chain D: S.570, S.573, H.574, R.577, Y.588, R.591, S.608, S.610, G.611, H.612, N.615, E.654 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:S.570, D:S.573, D:Y.588, D:S.610, D:G.611, D:H.612, D:H.612, D:N.615, D:E.654, D:E.654 Salt bridges: D:H.574, D:R.577, D:R.591

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

EDO.2: 4 residues within 4Å: Chain A: H.718, T.720, H.797, T.799 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.718, A:T.720, A:T.799 EDO.5: 4 residues within 4Å: Chain B: H.718, T.720, H.797, T.799 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.718, B:T.720, B:T.799 EDO.8: 4 residues within 4Å: Chain C: H.718, T.720, H.797, T.799 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.718 EDO.11: 4 residues within 4Å: Chain D: H.718, T.720, H.797, T.799 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.718

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: M.1, T.40, H.41, S.537, L.538, A.539, R.571 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.1, A:A.539 Water bridges: A:T.39 Salt bridges: A:H.41, A:R.571 SO4.6: 6 residues within 4Å: Chain B: M.1, H.41, S.537, L.538, A.539, R.571 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.539 Salt bridges: B:H.41, B:R.571 SO4.9: 7 residues within 4Å: Chain C: M.1, T.40, H.41, S.537, L.538, A.539, R.571 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:M.1, C:A.539 Water bridges: C:T.39 Salt bridges: C:H.41, C:R.571 SO4.12: 6 residues within 4Å: Chain D: M.1, H.41, S.537, L.538, A.539, R.571 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.539 Salt bridges: D:H.41, D:R.571

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, D. et al., 2.7 angstrom cryo-EM structure of rotavirus core protein VP3, a unique capping machine with a helicase activity. Sci Adv (2020)

Release Date

2020-03-04

Peptides

Protein VP3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

Protein VP3

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