SMTL ID : 3f1j.1

Crystal structure of the Borna disease virus matrix protein (BDV-M) reveals RNA binding properties

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

4 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.1: 7 residues within 4Å: Chain A: Q.36, F.37, H.112 Chain C: K.111, N.115 Ligands: C5P.9, C5P.13 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.36, A:F.37, A:F.37, C:N.115 pi-Stacking: A:F.37, A:H.112 C5P.5: 7 residues within 4Å: Chain B: Q.36, F.37, H.112 Chain D: K.111, N.115 Ligands: C5P.9, C5P.13 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:N.115, B:Q.36, B:F.37, B:F.37 pi-Stacking: B:F.37, B:H.112 C5P.9: 7 residues within 4Å: Chain B: K.111, N.115 Chain C: Q.36, F.37, H.112 Ligands: C5P.1, C5P.5 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.36, C:F.37, C:F.37, B:N.115 pi-Stacking: C:F.37, C:H.112 C5P.13: 7 residues within 4Å: Chain A: K.111, N.115 Chain D: Q.36, F.37, H.112 Ligands: C5P.1, C5P.5 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Q.36, D:F.37, D:F.37, A:N.115 pi-Stacking: D:F.37, D:H.112

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

SO4.2: 2 residues within 4Å: Chain A: R.126, N.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.127, A:N.127 Salt bridges: A:R.126 SO4.3: 1 residues within 4Å: Chain A: Y.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.93 Water bridges: A:K.13 SO4.4: 1 residues within 4Å: Chain A: K.55 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.55 SO4.6: 2 residues within 4Å: Chain B: R.126, N.127 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.127, B:N.127 Salt bridges: B:R.126 SO4.7: 1 residues within 4Å: Chain B: Y.93 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.13 SO4.8: 1 residues within 4Å: Chain B: K.55 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.55 SO4.10: 2 residues within 4Å: Chain C: R.126, N.127 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.127, C:N.127 Salt bridges: C:R.126 SO4.11: 1 residues within 4Å: Chain C: Y.93 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.13 SO4.12: 1 residues within 4Å: Chain C: K.55 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.55 SO4.14: 2 residues within 4Å: Chain D: R.126, N.127 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.127, D:N.127 Salt bridges: D:R.126 SO4.15: 1 residues within 4Å: Chain D: Y.93 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.93 Water bridges: D:K.13 SO4.16: 1 residues within 4Å: Chain D: K.55 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neumann, P. et al., Crystal structure of the Borna disease virus matrix protein (BDV-M) reveals ssRNA binding properties. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-02-03

Peptides

Matrix protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Matrix protein