SMTL ID : 7ckf.1

The N-terminus of interferon-inducible antiviral protein-dimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.53, T.76 Ligands: GDP.2, AF3.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.53, A:T.76 MG.4: 5 residues within 4Å: Chain B: S.53, T.76, T.99 Ligands: GDP.5, AF3.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.53, B:T.76

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 18 residues within 4Å: Chain A: R.49, T.50, G.51, K.52, S.53, Y.54, V.68, A.69, S.70, R.182, D.183, L.239, P.240, L.246, A.247, L.249 Ligands: MG.1, AF3.3 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.49, A:T.50, A:G.51, A:K.52, A:S.53, A:Y.54, A:A.69, A:R.182, A:L.249 Water bridges: A:R.182, A:D.183, A:D.183, A:K.244, A:A.247, B:N.133 Salt bridges: A:R.49, A:R.49, A:K.52, A:D.183 GDP.5: 18 residues within 4Å: Chain B: R.49, T.50, G.51, K.52, S.53, Y.54, V.68, A.69, S.70, R.182, D.183, L.239, P.240, L.246, A.247, L.249 Ligands: MG.4, AF3.6 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.49, B:T.50, B:G.51, B:K.52, B:S.53, B:Y.54, B:A.69, B:A.69, B:R.182 Water bridges: B:D.183, B:D.238, B:A.247, A:N.133 Salt bridges: B:R.49, B:R.49, B:K.52, B:D.183

2 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 9 residues within 4Å: Chain A: Y.48, R.49, K.52, S.74, H.75, T.76, G.101 Ligands: MG.1, GDP.2 No protein-ligand interaction detected (PLIP) AF3.6: 9 residues within 4Å: Chain B: Y.48, R.49, K.52, S.74, H.75, T.76, G.101 Ligands: MG.4, GDP.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, W. et al., Structural basis for GTP-induced dimerization and antiviral function of guanylate-binding proteins. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-05-05

Peptides

Guanylate-binding protein 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Guanylate-binding protein 5