SMTL ID : 5c3p.4 (3 other biounits)

Crystal structure of the full-length Neurospora crassa T7H in complex with alpha-KG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.216, D.218, H.273 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.216, A:D.218, A:H.273, H2O.1

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 12 residues within 4Å: Chain A: R.192, L.194, Y.196, H.216, D.218, L.225, H.273, V.275, R.288, S.290, F.294 Ligands: NI.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.194, A:L.225, A:V.275 Hydrogen bonds: A:Y.196, A:S.290 Salt bridges: A:K.120, A:R.192, A:H.216, A:R.288

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: E.10, F.242, I.243, D.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.10, A:D.244 EDO.4: 4 residues within 4Å: Chain A: E.10, D.11, Q.241, I.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.241 EDO.5: 6 residues within 4Å: Chain A: T.44, K.236, S.237, P.238, K.269, T.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.236 Water bridges: A:G.240, A:S.270 EDO.6: 4 residues within 4Å: Chain A: R.262, K.317, Y.318, E.319 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.262, A:E.319 Water bridges: A:R.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi. Nucleic Acids Res. (2015)

Release Date

2015-10-21

Peptides

Thymine dioxygenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Thymine dioxygenase

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