SMTL ID : 5vsm.2 (1 other biounit)

Crystal structure of viperin with bound [4Fe-4S] cluster, 5'-deoxyadenosine, and L-methionine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 10 residues within 4Å: Chain A: C.40, Y.42, C.44, C.47, G.82, N.114, R.150, R.221 Ligands: 5AD.2, MET.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.40, A:C.44, A:C.47, MET.3

1 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.2: 16 residues within 4Å: Chain A: F.46, C.47, F.48, V.112, S.136, R.150, N.178, V.180, F.205, Q.206, C.207, L.208, N.214, Y.258 Ligands: SF4.1, MET.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:F.46, A:F.48, A:S.136, A:S.136, A:R.150, A:R.150, A:N.178, A:L.208, A:N.214 pi-Stacking: A:F.48, A:F.48

1 x MET: METHIONINE(Non-covalent)

MET.3: 12 residues within 4Å: Chain A: H.49, S.80, G.81, G.82, E.83, V.112, S.113, N.114, S.136, R.150 Ligands: SF4.1, 5AD.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.112 Hydrogen bonds: A:E.83, A:S.113, A:S.136 Salt bridges: A:R.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenwick, M.K. et al., Structural studies of viperin, an antiviral radical SAM enzyme. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-06-14

Peptides

Radical S-adenosyl methionine domain-containing protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Radical S-adenosyl methionine domain-containing protein 2

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