SMTL ID : 9cf4.1

Crystal structure of the dimeric transaminase DoeD from C. salexigens DSM 3043.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: Y.187, Y.188, E.199, V.237, P.238, P.239, P.240, E.377, R.379 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.199, A:P.238, A:E.377 Water bridges: A:Y.187, A:Y.187, A:Y.187 GOL.2: 8 residues within 4Å: Chain A: G.109, M.110, P.283, D.284, G.305, D.306, R.307, V.308 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.284, A:D.306, A:R.307, A:R.307 Water bridges: A:V.308 GOL.3: 7 residues within 4Å: Chain A: V.88, G.89, H.90 Chain B: P.31, G.32, R.33, M.414 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.88, A:H.90, B:R.33, B:R.33 GOL.4: 5 residues within 4Å: Chain A: L.215, E.217, G.218, P.219, E.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.220 Water bridges: A:E.220 GOL.5: 9 residues within 4Å: Chain B: Y.187, Y.188, E.199, V.237, P.238, P.239, P.240, E.377, R.379 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.199, B:P.238, B:E.377 Water bridges: B:Y.187, B:Y.188, B:Y.188

1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.6: 14 residues within 4Å: Chain A: W.326, T.327 Chain B: S.118, G.119, S.120, N.123, Y.152, H.153, G.154, E.228, D.261, V.263, V.264, K.290 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.152, B:E.228, B:V.263 Hydrogen bonds: B:G.119, B:S.120, B:S.120, B:S.120, B:K.290, A:T.327, A:T.327 Water bridges: B:E.228, B:T.233, A:Y.328 Salt bridges: B:K.290 pi-Stacking: B:Y.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skogvold, A.C.A. et al., Crystal structure and biochemical analysis of the dimeric transaminase DoeD provides insights into ectoine degradation. Febs J. (2025)

Release Date

2025-03-12

Peptides

Aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aminotransferase