SMTL ID : 5y9r.1

Crystal structure of the oligomerization domain of NSP4 from rotavirus strain MF66

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

1 x CD: CADMIUM ION(Non-covalent)

CD.1: 3 residues within 4Å: Chain A: D.21 Chain B: H.38 Chain D: E.32 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:H.38, A:D.21, D:E.32, D:E.32, H2O.2

2 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 2 residues within 4Å: Chain A: H.38 Chain B: D.21 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.21, B:D.21, A:H.38, H2O.1, H2O.1 NI.6: 3 residues within 4Å: Chain A: E.29, E.32 Chain D: H.38 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: A:E.29, A:E.32, D:H.38, H2O.1, H2O.1, H2O.1

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 1 residues within 4Å: Chain B: D.7 No protein-ligand interaction detected (PLIP) EDO.4: 2 residues within 4Å: Chain C: E.29, E.32 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.36, C:R.36 EDO.5: 2 residues within 4Å: Chain C: D.21, T.25 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.25 EDO.7: 3 residues within 4Å: Chain D: E.29, E.32, L.33 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suguna, K. et al., New tetrameric forms of the rotavirus NSP4 with antiparallel helices. To Be Published

Release Date

2018-09-05

Peptides

Nonstructural protein 4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
C

D
A

Nonstructural protein 4