SMTL ID : 2i9f.2 (1 other biounit)

Structure of the equine arterivirus nucleocapsid protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: H.7, H.8, E.9 Chain F: T.24, N.28, T.56 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:E.9, F:N.28 GOL.2: 2 residues within 4Å: Chain A: K.57, R.61 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.57, A:R.61 Water bridges: A:K.57 GOL.7: 6 residues within 4Å: Chain B: T.24, N.28, T.56 Chain E: H.7, H.8, E.9 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:N.28, E:H.8, E:E.9 GOL.8: 2 residues within 4Å: Chain E: K.57, R.61 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.57, E:R.61 Water bridges: E:K.57

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain B: H.37, V.51, S.52 Chain F: H.37, S.52 Ligands: CL.9 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain B: H.37, S.52 Chain F: H.37, V.51, S.52 Ligands: CL.3 Ligand excluded by PLIP

2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.4: 6 residues within 4Å: Chain B: H.7, H.8, E.9 Chain C: T.24, N.28, T.56 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.9 DTT.10: 6 residues within 4Å: Chain F: H.7, H.8, E.9 Chain G: T.24, N.28, T.56 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:H.8, F:E.9

4 x NA: SODIUM ION(Non-functional Binders)

NA.5: 5 residues within 4Å: Chain C: A.42, D.43, G.46, L.47, T.48 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.46 Water bridges: C:G.45 NA.6: 5 residues within 4Å: Chain A: W.53, V.54 Chain C: G.36, H.37, G.38 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Water bridges: C:G.38 Hydrogen bonds: A:V.54, A:V.54 NA.11: 5 residues within 4Å: Chain G: A.42, D.43, G.46, L.47, T.48 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:T.48, G:T.48 Water bridges: G:G.45 NA.12: 5 residues within 4Å: Chain E: W.53, V.54 Chain G: G.36, H.37, G.38 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain G Hydrogen bonds: E:V.54, E:V.54 Water bridges: G:G.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deshpande, A. et al., Structure of the equine arteritis virus nucleocapsid protein reveals a dimer-dimer arrangement. Acta Crystallogr.,Sect.D (2007)

Release Date

2007-05-01

Peptides

Nucleocapsid: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Nucleocapsid

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