SMTL ID : 6vso.3 (2 other biounits)

DengueV-2 Capsid Structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

8 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 5 residues within 4Å: Chain A: R.63, R.66 Chain B: L.73, N.77 Ligands: GOL.6 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.63, A:R.63, A:R.66, A:R.66, B:N.77 NO3.2: 5 residues within 4Å: Chain A: Q.20, T.43, A.44, G.45 Chain B: V.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.43, A:T.43, A:A.44, A:G.45 NO3.3: 6 residues within 4Å: Chain A: F.14, G.17, M.18, L.19, Q.20 Chain B: V.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.17, A:L.19 NO3.4: 4 residues within 4Å: Chain A: L.25, R.49, I.53, K.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.49, A:K.54 NO3.5: 3 residues within 4Å: Chain A: R.13, L.27 Chain B: L.38 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.13, B:L.38 NO3.8: 5 residues within 4Å: Chain A: L.73, N.77 Chain B: I.59, R.63, R.66 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.63, B:R.66, B:R.66, A:N.77, A:N.77 NO3.9: 4 residues within 4Å: Chain B: L.25, R.49, I.53, K.54 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.49, B:R.49, B:K.54 NO3.10: 3 residues within 4Å: Chain B: R.63, R.66, K.67 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.66, B:R.66

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: R.63, R.66 Ligands: NO3.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.66 GOL.7: 1 residues within 4Å: Chain A: K.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.26, A:K.26 GOL.11: 4 residues within 4Å: Chain A: R.66 Chain B: R.66, K.67, G.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.66, A:R.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, H. et al., A cocrystal structure of dengue capsid protein in complex of inhibitor. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-07-15

Peptides

Capsid premembrane protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Capsid premembrane protein

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