SMTL ID : 8w0o.2 (1 other biounit)

GDH-105 crystal structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 25 residues within 4Å: Chain A: G.14, S.17, G.18, L.19, Y.39, Q.43, G.64, D.65, V.66, N.92, A.93, G.94, T.115, M.143, S.144, S.145, Y.158, K.162, P.188, G.189, A.190, I.191, T.193, I.195, N.196 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:P.188 Hydrogen bonds: A:S.17, A:S.17, A:S.17, A:L.19, A:Q.43, A:D.65, A:D.65, A:V.66, A:N.92, A:N.92, A:G.94, A:Y.158, A:K.162, A:I.191, A:I.191, A:T.193, A:N.196 Water bridges: A:G.14, A:A.16, A:G.20, A:Y.39, A:G.94, A:L.95, A:T.193, A:I.195 pi-Stacking: A:Y.39, A:Y.39 NAD.3: 25 residues within 4Å: Chain B: G.14, S.17, G.18, L.19, Y.39, Q.43, G.64, D.65, V.66, N.92, A.93, G.94, T.115, M.143, S.144, S.145, Y.158, K.162, P.188, G.189, A.190, I.191, T.193, I.195, N.196 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:P.188 Hydrogen bonds: B:S.17, B:S.17, B:S.17, B:L.19, B:Q.43, B:D.65, B:V.66, B:N.92, B:N.92, B:G.94, B:K.162, B:I.191, B:I.191, B:T.193, B:N.196 Water bridges: B:G.14, B:A.16, B:G.20, B:G.94, B:L.95, B:I.195 pi-Stacking: B:Y.39, B:Y.39 NAD.4: 25 residues within 4Å: Chain C: G.14, S.17, G.18, L.19, Y.39, Q.43, G.64, D.65, V.66, N.92, A.93, G.94, T.115, M.143, S.144, S.145, Y.158, K.162, P.188, G.189, A.190, I.191, T.193, I.195, N.196 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:P.188 Hydrogen bonds: C:S.17, C:S.17, C:S.17, C:S.17, C:L.19, C:Q.43, C:D.65, C:D.65, C:V.66, C:N.92, C:N.92, C:G.94, C:Y.158, C:K.162, C:I.191, C:I.191, C:N.196 Water bridges: C:G.14, C:A.16, C:G.20, C:Y.39, C:G.94, C:L.95, C:T.115, C:T.115, C:T.193, C:I.195 pi-Stacking: C:Y.39, C:Y.39 NAD.6: 25 residues within 4Å: Chain D: G.14, S.17, G.18, L.19, Y.39, Q.43, G.64, D.65, V.66, N.92, A.93, G.94, T.115, M.143, S.144, S.145, Y.158, K.162, P.188, G.189, A.190, I.191, T.193, I.195, N.196 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:P.188 Hydrogen bonds: D:S.17, D:S.17, D:S.17, D:L.19, D:Q.43, D:D.65, D:V.66, D:N.92, D:N.92, D:G.94, D:K.162, D:I.191, D:I.191, D:N.196 Water bridges: D:G.14, D:A.16, D:G.20, D:Y.39, D:G.94, D:L.95, D:T.115, D:T.115, D:I.195 pi-Stacking: D:Y.39, D:Y.39

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: Y.253, P.254, S.255 Chain B: Y.253, P.254, S.255 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain C: Y.253, P.254, S.255 Chain D: Y.253, P.254, S.255 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yi, X. et al., Enhancing the Imine Reductase Activity of a Promiscuous Glucose Dehydrogenase for Scalable Manufacturing of a Chiral Neprilysin Inhibitor Precursor. Acs Catalysis (2024)

Release Date

2024-07-24

Peptides

Dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
F

Dehydrogenase

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