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

Core (C) protein from West Nile Virus, subtype Kunjin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-octamer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: T.22 Chain C: T.22 Ligands: PO4.3, CA.5, PO4.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Metal complexes: A:T.22, C:T.22 CA.5: 5 residues within 4Å: Chain A: T.22 Chain C: T.22 Ligands: CA.1, PO4.3, PO4.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Metal complexes: A:T.22, C:T.22 CA.9: 3 residues within 4Å: Chain F: T.22 Chain H: T.22 Ligands: CA.12 No protein-ligand interaction detected (PLIP) CA.12: 3 residues within 4Å: Chain F: T.22 Chain H: T.22 Ligands: CA.9 No protein-ligand interaction detected (PLIP)

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

CL.2: 6 residues within 4Å: Chain A: R.10, S.14, G.20, P.21 Chain C: R.10 Ligands: CL.6 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: R.10 Chain C: R.10, S.14, G.20, P.21 Ligands: CL.2 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain F: R.10 Chain H: R.10, S.14, G.20, P.21 Ligands: CL.13 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain F: R.10, S.14, G.20, P.21 Chain H: R.10 Ligands: CL.10 Ligand excluded by PLIP

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: T.22, T.54 Chain C: T.22, T.54, H.58 Ligands: CA.1, CA.5, PO4.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.22 PO4.7: 8 residues within 4Å: Chain A: T.22, T.54, H.58 Chain C: T.22, T.54 Ligands: CA.1, PO4.3, CA.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.22

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 6 residues within 4Å: Chain A: L.8, F.31, F.32 Chain B: F.31 Chain E: L.3, K.9 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:K.9 Hydrophobic interactions: A:F.31, A:F.32 PG4.8: 6 residues within 4Å: Chain C: L.8, F.31, F.32 Chain D: F.31 Chain G: L.3, K.9 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:F.31, C:F.32 Hydrogen bonds: G:K.9 PG4.11: 7 residues within 4Å: Chain E: G.7, L.8, L.15, F.32 Chain F: L.8, F.31, F.32 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:F.31, F:F.32 PG4.14: 7 residues within 4Å: Chain G: G.7, L.8, L.15, F.32 Chain H: L.8, F.31, F.32 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:F.31, H:F.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dokland, T. et al., West nile virus core protein; tetramer structure and ribbon formation. Structure (2004)

Release Date

2004-08-09

Peptides

Core protein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
C

F
D

G
C

H
D

Core protein

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