SMTL ID : 8hpe.1

Crystal structure of Leucine dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.22 Å

Oligo State

homo-octamer

Ligands

52 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: R.46, R.62, N.263, N.264 Ligand excluded by PLIP SO4.2: 5 residues within 4Å: Chain A: K.65, G.66, Y.69, Y.286, D.338 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: K.93, S.94, F.98, D.124, I.127 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: G.184, N.185 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: P.150, H.189, K.192, H.193 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: N.226, Y.229 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: H.34, D.35, T.68, Y.69, I.345 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: G.26, K.28, I.86, D.92 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: R.46, W.48, Y.50, D.59 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: T.121, V.122 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain B: R.46, R.62, L.63, N.263, N.264 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain B: R.357 Chain C: N.358, H.360 Chain G: Q.106 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: Q.106 Chain F: N.358, H.360 Chain G: R.357 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain C: R.46, R.62, N.263, N.264 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain C: K.65, G.66, Y.69, Y.286, D.338 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain C: K.93, S.94, F.98, D.124, I.127 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain C: G.184, N.185 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain C: P.150, H.189, K.192, H.193 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain C: N.226, Y.229 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain C: H.34, D.35, T.68, Y.69, I.345 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain C: G.26, K.28, I.86, D.92 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain C: R.46, W.48, Y.50, D.59 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain C: T.121, V.122 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain D: R.46, R.62, L.63, N.263, N.264 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain A: N.358, H.360 Chain D: R.357 Chain E: Q.106 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain D: Q.106 Chain E: R.357 Chain H: N.358, H.360 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain E: R.46, R.62, N.263, N.264 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain E: K.65, G.66, Y.69, Y.286, D.338 Ligand excluded by PLIP SO4.33: 5 residues within 4Å: Chain E: K.93, S.94, F.98, D.124, I.127 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain E: G.184, N.185 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain E: P.150, H.189, K.192, H.193 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain E: N.226, Y.229 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain E: H.34, D.35, T.68, Y.69, I.345 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain E: G.26, K.28, I.86, D.92 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain E: R.46, W.48, Y.50, D.59 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain E: T.121, V.122 Ligand excluded by PLIP SO4.42: 5 residues within 4Å: Chain F: R.46, R.62, L.63, N.263, N.264 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain A: Q.106 Chain F: R.357 Chain G: N.358, H.360 Ligand excluded by PLIP SO4.44: 4 residues within 4Å: Chain A: R.357 Chain D: N.358, H.360 Chain F: Q.106 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain G: R.46, R.62, N.263, N.264 Ligand excluded by PLIP SO4.47: 5 residues within 4Å: Chain G: K.65, G.66, Y.69, Y.286, D.338 Ligand excluded by PLIP SO4.48: 5 residues within 4Å: Chain G: K.93, S.94, F.98, D.124, I.127 Ligand excluded by PLIP SO4.49: 2 residues within 4Å: Chain G: G.184, N.185 Ligand excluded by PLIP SO4.50: 4 residues within 4Å: Chain G: P.150, H.189, K.192, H.193 Ligand excluded by PLIP SO4.51: 2 residues within 4Å: Chain G: N.226, Y.229 Ligand excluded by PLIP SO4.52: 5 residues within 4Å: Chain G: H.34, D.35, T.68, Y.69, I.345 Ligand excluded by PLIP SO4.53: 4 residues within 4Å: Chain G: G.26, K.28, I.86, D.92 Ligand excluded by PLIP SO4.54: 4 residues within 4Å: Chain G: R.46, W.48, Y.50, D.59 Ligand excluded by PLIP SO4.55: 2 residues within 4Å: Chain G: T.121, V.122 Ligand excluded by PLIP SO4.57: 5 residues within 4Å: Chain H: R.46, R.62, L.63, N.263, N.264 Ligand excluded by PLIP SO4.58: 4 residues within 4Å: Chain C: Q.106 Chain E: N.358, H.360 Chain H: R.357 Ligand excluded by PLIP SO4.59: 4 residues within 4Å: Chain B: N.358, H.360 Chain C: R.357 Chain H: Q.106 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 5 residues within 4Å: Chain A: R.103 Chain B: Y.355 Chain G: G.359, H.360, D.361 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain G Hydrogen bonds: A:R.103, A:R.103, G:D.361, G:D.361 GOL.15: 5 residues within 4Å: Chain B: S.94, E.95, A.96 Chain F: R.344, S.347 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.95, B:E.95 GOL.26: 5 residues within 4Å: Chain C: R.103 Chain D: Y.355 Chain E: G.359, H.360, D.361 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:R.103, C:R.103, E:D.361, E:D.361 GOL.30: 5 residues within 4Å: Chain D: S.94, E.95, A.96 Chain H: R.344, S.347 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.95, D:E.95 GOL.41: 5 residues within 4Å: Chain A: G.359, H.360, D.361 Chain E: R.103 Chain F: Y.355 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:R.103, E:R.103, A:D.361, A:D.361 GOL.45: 5 residues within 4Å: Chain D: R.344, S.347 Chain F: S.94, E.95, A.96 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.95, F:E.95 GOL.56: 5 residues within 4Å: Chain C: G.359, H.360, D.361 Chain G: R.103 Chain H: Y.355 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain C Hydrogen bonds: G:R.103, G:R.103, C:D.361, C:D.361 GOL.60: 5 residues within 4Å: Chain B: R.344, S.347 Chain H: S.94, E.95, A.96 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:E.95, H:E.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, X. et al., A Tri-Enzyme Cascade for Efficient Production of L-2-Aminobutyrate from L-Threonine. Chembiochem (2023)

Release Date

2024-03-20

Peptides

Leucine dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Leucine dehydrogenase

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