SMTL ID : 4q5o.1

Crystal structure of EctD from S. alaskensis with 2-oxoglutarate and 5-hydroxyectoine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

homo-dimer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: H.152, D.154, H.253 Ligands: AKG.2, 6CS.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.152, A:D.154, A:H.253 FE.4: 5 residues within 4Å: Chain B: H.152, D.154, H.253 Ligands: AKG.5, 6CS.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.152, B:D.154, B:D.154, B:H.253

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

AKG.2: 8 residues within 4Å: Chain A: R.137, N.139, K.141, F.149, H.152, H.253, F.268 Ligands: FE.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.149 Hydrogen bonds: A:N.139 Salt bridges: A:R.137, A:K.141, A:K.141 AKG.5: 12 residues within 4Å: Chain B: R.137, N.139, F.149, H.152, D.154, L.186, H.253, S.255, R.264, F.268 Ligands: FE.4, 6CS.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.149, B:L.186, B:F.268 Hydrogen bonds: B:N.139, B:D.154, B:S.255, B:S.255 Salt bridges: B:R.137, B:K.141, B:R.264

2 x 6CS: (4S,5S)-5-HYDROXY-2-METHYL-1,4,5,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID(Covalent)

6CS.3: 9 residues within 4Å: Chain A: Q.135, R.137, F.149, H.152, D.154, W.158, H.253, R.288 Ligands: FE.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.135, A:Q.135, A:R.137, A:R.288 Salt bridges: A:H.152 6CS.6: 9 residues within 4Å: Chain B: Q.135, R.137, H.152, D.154, T.157, W.158, R.288 Ligands: FE.4, AKG.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.135, B:R.137, B:R.288 Salt bridges: B:H.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoppner, A. et al., Crystal structure of the ectoine hydroxylase, a snapshot of the active site. J.Biol.Chem. (2014)

Release Date

2014-09-10

Peptides

Ectoine hydroxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ectoine hydroxylase

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