SMTL ID : 3sng.1

X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

monomer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 10 residues within 4Å: Chain A: W.55, L.59, D.85, M.86, G.90, A.91, N.94, F.95, Q.98, R.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.110 NAG-NAG-BMA.3: 10 residues within 4Å: Chain A: Y.171, Y.172, L.179, D.182, I.183, N.186, I.191, N.240, L.243, M.247 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.171

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 9 residues within 4Å: Chain A: P.30, Y.32, L.40, W.43, Y.53, N.112, E.115, L.118 Ligands: CL.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.40, A:L.118 Hydrogen bonds: A:Y.32

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 7 residues within 4Å: Chain A: W.1, H.6, D.45, H.122, D.126, H.132 Ligands: ZN.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:W.1, A:H.6, A:D.126, H2O.1 ZN.5: 5 residues within 4Å: Chain A: D.45, H.60, H.122, D.126 Ligands: ZN.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.45, A:H.60, A:H.122, A:D.126, H2O.1 ZN.6: 4 residues within 4Å: Chain A: H.132, H.156, D.160 Ligands: SO4.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.132, A:H.156, A:D.160, A:D.160

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 8 residues within 4Å: Chain A: R.48, H.60, F.61, H.132, N.142, H.156, D.160 Ligands: ZN.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.142 Salt bridges: A:R.48, A:H.132, A:H.156

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

CL.8: 2 residues within 4Å: Chain A: W.43 Ligands: NAG-NAG-BMA-MAN.2 Ligand excluded by PLIP

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.9: 3 residues within 4Å: Chain A: Q.93, N.204, F.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koval, T. et al., Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis. Acta Crystallogr.,Sect.D (2013)

Release Date

2012-07-04

Peptides

nuclease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

nuclease