SMTL ID : 2gmu.1

Crystal structure of E coli GDP-4-keto-6-deoxy-D-mannose-3-dehydratase complexed with PLP-glutamate ketimine intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: E.377, D.380 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.377, H2O.4, H2O.4, H2O.4, H2O.4

2 x PDG: N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC ACID(Non-covalent)

PDG.2: 19 residues within 4Å: Chain A: 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, H.190, G.197 Chain B: H.217, W.219, N.250, R.252 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.90, A:W.90 Hydrogen bonds: A:G.58, A:S.59, A:S.59, A:N.62, A:E.164, A:S.185, A:S.185, B:N.250 Salt bridges: A:H.190, B:H.217, B:H.217, B:R.252 PDG.3: 19 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, H.190, G.197 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.90 Hydrogen bonds: B:G.58, B:S.59, B:S.59, B:N.62, B:E.164, B:E.164, B:S.185, B:S.185, A:N.250 Salt bridges: B:H.190, A:H.217, A:H.217, A:R.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, P.D. et al., The structure of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: a unique coenzyme B6-dependent enzyme. Protein Sci. (2006)

Release Date

2006-09-05

Peptides

Putative pyridoxamine 5-phosphate-dependent dehydrase, WbdK: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative pyridoxamine 5-phosphate-dependent dehydrase, WbdK

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