SMTL ID : 2b5w.1

Crystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.38, H.63, E.64, E.150 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.38, A:H.63, A:E.64 ZN.9: 4 residues within 4Å: Chain B: C.38, H.63, E.64, E.150 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.38, B:H.63, B:E.64

2 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 6 residues within 4Å: Chain A: S.228, P.232, F.252, K.254, H.255 Ligands: NAP.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.228 Salt bridges: A:K.254, A:H.255 FLC.10: 6 residues within 4Å: Chain B: S.228, P.232, F.252, K.254, H.255 Ligands: NAP.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.228 Salt bridges: B:K.254, B:H.255

10 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.3: 2 residues within 4Å: Chain A: D.344, T.347 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.344, A:T.347 K.4: 4 residues within 4Å: Chain A: D.172, P.173, K.197, G.198 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.172, A:P.173, A:K.197, A:G.198 K.5: 1 residues within 4Å: Chain A: T.315 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.315 K.6: 3 residues within 4Å: Chain A: P.237, D.238, Y.240 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:P.237, A:Y.240 K.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.11: 2 residues within 4Å: Chain B: D.344, T.347 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.344, B:T.347 K.12: 4 residues within 4Å: Chain B: D.172, P.173, K.197, G.198 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.172, B:P.173, B:K.197, B:G.198 K.13: 1 residues within 4Å: Chain B: T.315 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.315 K.14: 3 residues within 4Å: Chain B: P.237, D.238, Y.240 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:P.237, B:Y.240 K.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.8: 28 residues within 4Å: Chain A: C.38, G.39, T.40, E.43, I.154, G.180, N.181, G.182, S.183, L.184, L.205, G.206, R.207, R.208, S.228, A.249, T.250, G.251, F.252, H.255, L.272, G.273, V.274, S.301, V.302, N.303 Chain B: V.292 Ligands: FLC.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.154, A:L.184 Hydrogen bonds: A:G.39, A:E.43, A:N.181, A:N.181, A:S.183, A:L.184, A:R.207, A:R.208, A:S.228, A:L.272, A:V.274, A:N.303 Salt bridges: A:R.207, A:R.208 pi-Cation interactions: A:R.207 NAP.16: 28 residues within 4Å: Chain A: V.292 Chain B: C.38, G.39, T.40, E.43, I.154, G.180, N.181, G.182, S.183, L.184, L.205, G.206, R.207, R.208, S.228, A.249, T.250, G.251, F.252, H.255, L.272, G.273, V.274, S.301, V.302, N.303 Ligands: FLC.10 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.154, B:L.184 Hydrogen bonds: B:G.39, B:E.43, B:N.181, B:N.181, B:S.183, B:L.184, B:R.207, B:R.208, B:S.228, B:L.272, B:V.274, B:N.303 Salt bridges: B:R.207, B:R.208 pi-Cation interactions: B:R.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Britton, K.L. et al., Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-04-04

Peptides

glucose dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

glucose dehydrogenase