SMTL ID : 3b8x.1

Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase (ColD) H188N mutant with bound GDP-perosamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

8 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: K.173, T.177, D.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.173, A:T.177 NA.2: 4 residues within 4Å: Chain A: L.8, R.275, F.304, N.373 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.275, A:F.304, A:N.373 Water bridges: A:R.275 NA.3: 6 residues within 4Å: Chain A: E.82, K.105, A.124, T.126, S.128, T.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.82, A:T.126 NA.4: 5 residues within 4Å: Chain A: T.12, N.190, H.191, R.275, Q.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.275, A:R.275 Water bridges: A:S.10, A:Q.375 NA.9: 5 residues within 4Å: Chain B: L.8, A.9, S.189, F.304, N.373 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.275, B:N.373, B:N.373 Water bridges: B:R.275 NA.10: 2 residues within 4Å: Chain B: E.377, D.380 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.377 NA.11: 4 residues within 4Å: Chain A: F.244, V.245 Chain B: N.343, D.345 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.244 Water bridges: B:N.343 NA.12: 3 residues within 4Å: Chain B: K.173, T.177, D.203 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.173, B:D.203 Water bridges: B:D.203, B:D.203

2 x G4M: [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4-dihydroxy-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate(Non-covalent)

G4M.5: 29 residues within 4Å: Chain A: A.9, 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, Y.188, S.189, G.197, F.304, E.331, R.333, V.336 Chain B: K.28, M.29, F.30, T.31, H.217, R.221, F.242, N.250 35 PLIP interactions: 22 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:W.90, A:W.90, A:E.164, A:F.304, A:V.336 Hydrogen bonds: A:G.58, A:S.59, A:N.62, A:E.164, A:E.164, A:S.185, A:S.189, A:E.331, B:K.28, B:K.28, B:F.30, B:T.31, B:T.31, B:H.217, B:N.250 Water bridges: A:Y.188, A:Y.188, A:N.190, B:H.217, B:R.252, B:R.252 Salt bridges: A:R.333, A:R.333, A:R.333, B:H.217, B:R.221, B:R.221 pi-Stacking: A:Y.188, A:Y.188 pi-Cation interactions: A:Y.188 G4M.13: 28 residues within 4Å: Chain A: K.28, M.29, F.30, T.31, H.217, W.219, R.221, F.242, N.250 Chain B: L.8, S.57, G.58, S.59, N.62, W.90, T.92, T.93, D.161, C.163, E.164, S.185, F.187, Y.188, S.189, G.197, E.331, R.333, V.336 36 PLIP interactions: 22 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:W.90, B:E.164, B:V.336 Hydrogen bonds: B:S.57, B:G.58, B:S.59, B:N.62, B:T.93, B:E.164, B:S.185, B:S.189, B:E.331, A:K.28, A:K.28, A:F.30, A:T.31, A:T.31, A:H.217, A:N.250 Water bridges: B:Y.188, B:Y.188, B:E.196, B:R.333, B:R.333, A:H.217, A:R.221, A:R.221, A:R.252 Salt bridges: B:R.333, B:R.333, A:H.217, A:R.221, A:R.221 pi-Stacking: B:W.90, B:Y.188, B:Y.188

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

EDO.6: 7 residues within 4Å: Chain A: E.40, T.41, A.44, K.50, Y.51, A.52, Y.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.52, A:A.52 EDO.7: 8 residues within 4Å: Chain A: S.11, T.12, W.13, K.267, R.270, F.271, Q.375, I.376 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.11, A:R.270, A:R.270, A:Q.375 EDO.8: 4 residues within 4Å: Chain A: G.80, E.82, R.103, S.128 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.82, A:R.103 Water bridges: A:E.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, P.D. et al., GDP-4-Keto-6-deoxy-D-mannose 3-Dehydratase, Accommodating a Sugar Substrate in the Active Site. J.Biol.Chem. (2008)

Release Date

2007-11-27

Peptides

Pyridoxamine 5-phosphate-dependent dehydrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyridoxamine 5-phosphate-dependent dehydrase