SMTL ID : 6q2p.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

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

B3P.1: 4 residues within 4Å: Chain A: R.169, D.170, Y.171, K.172 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.169, A:D.170 Water bridges: A:D.170, A:D.170, A:Y.171, A:K.172

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

SF4.2: 8 residues within 4Å: Chain A: C.40, Y.42, C.44, C.47, G.82, N.114, R.150 Ligands: SAH.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.40, A:C.44, A:C.47, SAH.3

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

SAH.3: 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: SF4.2, CTP.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.112 Hydrogen bonds: A:F.46, A:F.48, A:E.83, A:E.83, A:S.113, A:S.136, A:S.136, A:R.150, 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

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.4: 24 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, I.210, M.254, K.255, Y.258, I.260, C.270, K.275, R.303, Y.307 Ligands: SAH.3 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:Y.258, A:I.260 Hydrogen bonds: A:N.33, A:N.33, A:N.33, A:N.78, A:S.80, A:S.110, A:N.178, A:K.255, A:Y.258, A:K.275 Water bridges: A:S.31, A:K.76, A:K.76, A:K.176, A:K.203, A:R.303, A:R.303, A:G.305 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

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

CL.5: 5 residues within 4Å: Chain A: F.233, P.248, E.249, S.250, K.253 Ligand excluded by PLIP

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
B

Radical S-adenosyl methionine domain-containing protein 2

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