SMTL ID : 3jb3.1 (3 other biounits)

Atomic model of cytoplasmic polyhedrosis virus with SAM, GTP and ATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

hetero-1-2-2-mer

Ligands

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

SAM.1: 17 residues within 4Å: Chain A: N.526, S.528, M.532, G.562, A.563, E.564, E.566, G.588, D.589, R.590, V.598, R.599, V.600, D.616, I.617, N.618, E.631 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.526, A:S.528, A:E.564, A:E.564, A:E.564, A:E.566, A:E.566, A:D.589, A:R.590, A:R.599, A:V.600, A:V.600, A:D.616, A:N.618 Salt bridges: A:E.564, A:D.616 SAM.2: 20 residues within 4Å: Chain A: K.838, Y.842, I.861, G.862, R.864, A.867, D.868, I.881, D.882, P.883, A.884, F.904, F.906, I.922, A.923, V.924, N.927, E.928, P.929, Y.992 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.923 Hydrogen bonds: A:Y.842, A:G.862, A:R.864, A:R.864, A:F.904, A:F.904, A:I.922

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

ATP.3: 7 residues within 4Å: Chain A: Y.268, R.271, S.301, D.302, Y.305, Y.316, Y.320 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.268, A:R.271, A:D.302, A:D.302, A:D.302, A:Y.305, A:Y.316, A:Y.320 Salt bridges: A:R.271, A:R.271 pi-Stacking: A:Y.305, A:Y.305 pi-Cation interactions: A:R.271, A:R.271

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.4: 17 residues within 4Å: Chain A: R.12, Y.59, N.61, W.115, M.116, P.165, I.166, T.167, Y.179, H.208, H.212, W.213, H.217, F.219, K.234, R.255 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.12, A:Y.59, A:N.61, A:N.61, A:N.61, A:Y.179 Salt bridges: A:H.208, A:H.212, A:H.217, A:K.234, A:K.234, A:R.255, A:R.255 pi-Stacking: A:Y.59

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: D.254 Ligands: GTP.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, X. et al., A putative ATPase mediates RNA transcription and capping in a dsRNA virus. Elife (2015)

Release Date

2015-08-12

Peptides

Structural protein VP3: A
Capsid protein VP1: BC
Viral structural protein 5: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Structural protein VP3

Capsid protein VP1

Viral structural protein 5

Related Entries With Identical Sequence