SMTL ID : 2oge.1 (1 other biounit)

x-ray structure of S. venezuelae DesV in its internal aldimine form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: Y.59, L.60 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: Y.247, H.249 Chain B: Y.113, Y.338 Ligands: EDO.8 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: Y.59, L.60 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: Y.338 Chain B: Y.247, H.249 Ligands: EDO.15 Ligand excluded by PLIP

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

NA.3: 2 residues within 4Å: Chain A: N.85 Chain B: N.85 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.259 Hydrogen bonds: B:N.85

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

EDO.4: 5 residues within 4Å: Chain A: P.31, F.32, L.33, D.34, D.333 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.32, A:L.33, A:L.33, A:D.333 EDO.5: 5 residues within 4Å: Chain A: A.74, Y.75, E.77, R.192, R.197 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.75, A:E.77, A:R.192, A:R.192, A:R.197 EDO.6: 7 residues within 4Å: Chain A: H.133, H.136, T.138, L.139, P.141, D.166, A.303 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.139 Water bridges: A:T.138, A:D.166, A:D.166, A:D.166 EDO.7: 7 residues within 4Å: Chain A: L.35, P.211, K.213, N.214, G.216, R.269, P.375 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.216, A:R.269 Water bridges: A:N.214, A:G.216, A:R.280 EDO.8: 6 residues within 4Å: Chain A: Y.241, K.246, Y.247, H.249 Chain B: Y.113 Ligands: CL.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.247, B:Y.113, B:Y.113 EDO.9: 6 residues within 4Å: Chain A: Y.113, Y.210, K.213 Chain B: Y.241, N.255, R.257 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:Y.113 Hydrogen bonds: B:R.257, B:R.257 EDO.10: 6 residues within 4Å: Chain A: D.47, I.50, A.51 Chain B: D.47, I.50, A.51 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.47, B:A.51, A:D.47, A:A.51 EDO.13: 5 residues within 4Å: Chain B: P.31, F.32, L.33, D.34, D.333 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.32, B:L.33, B:L.33, B:D.333, B:D.333 EDO.14: 6 residues within 4Å: Chain B: P.211, K.213, N.214, G.216, R.269, P.375 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.216, B:R.269, B:R.280 Water bridges: B:N.214, B:G.216 EDO.15: 6 residues within 4Å: Chain A: L.335, H.337, Y.338 Chain B: K.246, Y.247 Ligands: CL.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.246, B:K.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burgie, E.S. et al., Molecular architecture of DesV from Streptomyces venezuelae: A PLP-dependent transaminase involved in the biosynthesis of the unusual sugar desosamine. Protein Sci. (2007)

Release Date

2007-05-15

Peptides

Transaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transaminase

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