SMTL ID : 2r0t.1

Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase with a trapped PLP-glutamate geminal diamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x PGU: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid(Covalent)

PGU.1: 21 residues within 4Å: Chain A: S.57, G.58, S.59, N.62, S.89, W.90, T.92, T.93, V.135, D.161, C.163, E.164, S.185, F.187, K.190, G.197, R.333 Chain B: H.217, W.219, N.250, R.252 20 PLIP interactions: 15 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.90, A:V.135, A:F.187 Hydrogen bonds: A:S.57, A:G.58, A:S.59, A:N.62, A:T.93, A:E.164, A:E.164, A:S.185, A:S.185, B:N.250 Salt bridges: A:K.190, A:K.190, A:R.333, B:H.217, B:H.217, B:R.252 Water bridges: B:R.221 PGU.2: 20 residues within 4Å: Chain A: H.217, W.219, N.250, R.252 Chain B: S.57, G.58, S.59, N.62, S.89, W.90, T.92, T.93, D.161, C.163, E.164, S.185, F.187, K.190, G.197, R.333 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.90, B:W.90, B:W.90, B:F.187 Hydrogen bonds: B:S.57, B:G.58, B:S.59, B:N.62, B:T.93, B:E.164, B:S.185, A:N.250 Salt bridges: B:K.190, B:R.333, A:H.217, A:H.217, A:R.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, P.D. et al., A Structural Study of GDP-4-Keto-6-Deoxy-d-Mannose-3-Dehydratase: Caught in the Act of Geminal Diamine Formation. Biochemistry (2007)

Release Date

2007-12-18

Peptides

Pyridoxamine 5-phosphate-dependent dehydrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyridoxamine 5-phosphate-dependent dehydrase