SMTL ID : 6a3j.1

Levoglucosan dehydrogenase, complex with NADH and L-sorbose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 7 residues within 4Å: Chain A: F.33, W.185, S.194, R.196 Chain D: P.347, I.348 Ligands: SOE.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.194 Water bridges: A:W.195, A:R.196 MES.6: 7 residues within 4Å: Chain B: P.347, I.348 Chain C: F.33, W.185, S.194, R.196 Ligands: SOE.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.194 Water bridges: C:R.196, C:R.196

4 x SOE: alpha-L-sorbopyranose(Non-covalent)

SOE.2: 15 residues within 4Å: Chain A: F.33, K.124, Y.153, Y.181, Q.183, W.185, R.196, D.209, H.213, N.293, Y.355 Chain D: I.348, L.351 Ligands: MES.1, NAI.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.124, A:Y.181, A:Q.183, A:R.196, A:D.209, A:H.213, A:Y.355 Water bridges: A:N.152, A:D.209, A:R.286 SOE.4: 14 residues within 4Å: Chain B: F.33, K.124, Y.153, Y.181, Q.183, W.185, R.196, D.209, H.213, N.293, Y.355 Chain C: I.348, L.351 Ligands: NAI.5 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.124, B:K.124, B:Y.153, B:Y.181, B:Q.183, B:W.185, B:R.196, B:D.209, B:H.213 Water bridges: B:N.152, B:D.209 SOE.7: 14 residues within 4Å: Chain B: I.348, L.351 Chain C: K.124, Y.153, Y.181, Q.183, W.185, R.196, D.209, H.213, N.293, Y.355 Ligands: MES.6, NAI.8 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.124, C:Y.153, C:Y.181, C:Q.183, C:W.185, C:R.196, C:D.209, C:H.213 Water bridges: C:N.152, C:D.209 SOE.9: 14 residues within 4Å: Chain A: I.348, L.351 Chain D: F.33, K.124, Y.153, Y.181, Q.183, W.185, R.196, D.209, H.213, N.293, Y.355 Ligands: NAI.10 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.124, D:Y.181, D:Q.183, D:W.185, D:R.196, D:D.209, D:H.213, D:Y.355 Water bridges: D:N.152, D:R.286

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 20 residues within 4Å: Chain A: I.29, G.32, F.33, M.34, A.62, E.63, A.64, A.100, T.101, P.102, N.103, L.105, H.106, E.123, K.124, P.125, W.195, R.196, D.209 Ligands: SOE.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.32, A:F.33, A:M.34, A:T.101, A:N.103, A:K.124, A:K.124, A:R.196, A:D.209 Water bridges: A:G.35, A:E.63, A:W.85, A:N.103 Salt bridges: A:R.196 NAI.5: 22 residues within 4Å: Chain B: I.29, G.30, G.32, F.33, M.34, A.62, E.63, A.64, W.85, A.100, T.101, P.102, N.103, L.105, H.106, E.123, K.124, P.125, W.195, R.196, D.209 Ligands: SOE.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.32, B:F.33, B:M.34, B:T.101, B:N.103, B:K.124, B:K.124, B:R.196 Water bridges: B:G.35, B:E.63, B:N.103 Salt bridges: B:R.196 NAI.8: 22 residues within 4Å: Chain C: I.29, G.30, G.32, F.33, M.34, A.62, E.63, A.64, W.85, A.100, T.101, P.102, N.103, L.105, H.106, E.123, K.124, P.125, W.195, R.196, D.209 Ligands: SOE.7 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:F.33, C:M.34, C:T.101, C:N.103, C:K.124, C:K.124, C:R.196 Water bridges: C:G.32, C:G.35, C:N.103 Salt bridges: C:R.196 NAI.10: 21 residues within 4Å: Chain D: I.29, G.32, F.33, M.34, A.62, E.63, A.64, W.85, A.100, T.101, P.102, N.103, L.105, H.106, E.123, K.124, P.125, W.195, R.196, D.209 Ligands: SOE.9 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.31, D:G.32, D:F.33, D:M.34, D:T.101, D:N.103, D:K.124, D:K.124, D:R.196, D:D.209 Water bridges: D:G.35, D:W.85, D:W.85, D:N.103 Salt bridges: D:R.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugiura, M. et al., Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase. J. Biol. Chem. (2018)

Release Date

2018-09-26

Peptides

Putative dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative dehydrogenase

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