SMTL ID : 6q2q.1 (1 other biounit)

Crystal structure of mouse viperin bound to uridine triphosphate and S-adenosylhomocysteine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

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

SF4.1: 9 residues within 4Å: Chain A: C.40, Y.42, C.44, C.47, G.82, N.114, R.150, R.221 Ligands: SAH.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.40, A:C.44, A:C.47, SAH.2

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 22 residues within 4Å: Chain A: F.46, C.47, F.48, S.80, G.81, G.82, E.83, V.112, S.113, N.114, S.136, R.150, N.178, V.180, F.205, Q.206, C.207, L.208, N.214, M.254 Ligands: SF4.1, UTP.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:F.46, A:F.48, A:E.83, A:S.136, A:S.136, A:R.150, A:N.178, A:L.208, A:N.214 Salt bridges: A:R.150 pi-Stacking: A:F.48, A:F.48

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

CL.3: 4 residues within 4Å: Chain A: Q.152, G.153, K.154, K.155 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: K.70 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: P.248, E.249, S.250, K.253 Ligand excluded by PLIP

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.4: 23 residues within 4Å: Chain A: N.33, H.35, F.48, K.76, N.78, S.80, S.110, V.112, K.176, N.178, R.201, K.203, F.205, L.208, M.254, K.255, Y.258, I.260, C.270, K.275, R.303, Y.307 Ligands: SAH.2 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:N.33, A:N.78, A:N.78, A:S.80, A:S.80, A:S.110, A:N.178, A:K.275, A:K.275, A:Y.307 Water bridges: A:S.31, A:K.76, A:K.76, A:K.176, A:E.249, A:R.303, A:R.303 Salt bridges: A:K.76, A:K.76, A:K.176, A:K.176, A:K.176, A:R.201, A:K.203, A:K.203, A:K.203, A:R.303 pi-Stacking: A:F.48, A:Y.258

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.6: 4 residues within 4Å: Chain A: P.107, S.310, A.312, D.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.107, A:S.310 Water bridges: A:D.313, A:D.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenwick, M.K. et al., Structural Basis of the Substrate Selectivity of Viperin. Biochemistry (2020)

Release Date

2020-01-22

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Radical S-adenosyl methionine domain-containing protein 2

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