SMTL ID : 3hhw.1

Complex of a vesicular stomatitis virus empty capsid with the nucleocapsid-binding domain of the phosphoprotein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-10-10-mer

Ligands

12 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.1: 4 residues within 4Å: Chain F: K.82, G.98, D.99, T.100 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:K.82, F:K.82, F:T.100 Salt bridges: F:K.82, F:K.82 TAR.2: 4 residues within 4Å: Chain F: K.131, M.165, E.208, C.209 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:K.131 TAR.3: 6 residues within 4Å: Chain F: K.222, D.223, A.225, W.289, S.290, V.291 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:D.223, F:A.225, F:S.290, F:S.290, F:V.291 TAR.4: 7 residues within 4Å: Chain F: P.263, G.264, Q.265, E.266, D.268, K.269 Chain J: K.16 4 PLIP interactions: 1 interactions with chain J, 3 interactions with chain F Salt bridges: J:K.16 Hydrogen bonds: F:G.264, F:E.266, F:D.268 TAR.5: 9 residues within 4Å: Chain C: L.39, L.77, Q.80, A.81, K.84, Y.85 Chain H: T.360, G.361, T.365 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain H Hydrogen bonds: C:Y.85, H:T.365, H:T.365 TAR.6: 3 residues within 4Å: Chain F: D.391 Chain J: K.387, P.388 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain F Hydrogen bonds: J:K.387 Salt bridges: J:K.387, F:R.398 TAR.7: 4 residues within 4Å: Chain P: K.82, G.98, D.99, T.100 5 PLIP interactions: 5 interactions with chain P Hydrogen bonds: P:K.82, P:K.82, P:T.100 Salt bridges: P:K.82, P:K.82 TAR.8: 4 residues within 4Å: Chain P: K.131, M.165, E.208, C.209 1 PLIP interactions: 1 interactions with chain P Salt bridges: P:K.131 TAR.9: 6 residues within 4Å: Chain P: K.222, D.223, A.225, W.289, S.290, V.291 5 PLIP interactions: 5 interactions with chain P Hydrogen bonds: P:D.223, P:A.225, P:S.290, P:S.290, P:V.291 TAR.10: 7 residues within 4Å: Chain P: P.263, G.264, Q.265, E.266, D.268, K.269 Chain T: K.16 4 PLIP interactions: 1 interactions with chain T, 3 interactions with chain P Salt bridges: T:K.16 Hydrogen bonds: P:G.264, P:E.266, P:D.268 TAR.11: 9 residues within 4Å: Chain M: L.39, L.77, Q.80, A.81, K.84, Y.85 Chain R: T.360, G.361, T.365 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain R Hydrogen bonds: M:Y.85, R:T.365, R:T.365 TAR.12: 3 residues within 4Å: Chain P: D.391 Chain T: K.387, P.388 3 PLIP interactions: 1 interactions with chain P, 2 interactions with chain T Salt bridges: P:R.398, T:K.387 Hydrogen bonds: T:K.387

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Green, T.J. et al., Structure of the vesicular stomatitis virus nucleocapsid in complex with the nucleocapsid-binding domain of the small polymerase cofactor, P. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-07-28

Peptides

Phosphoprotein: ABCDEKLMNO
Nucleoprotein: FGHIJPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

K
A

L
B

M
C

N
D

O
E

F
K

G
L

H
M

I
N

J
O

P
K

Q
L

R
M

S
N

T
O

Phosphoprotein

Nucleoprotein

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