SMTL ID : 2oga.3 (2 other biounits)

X-ray crystal structure of S. venezuelae DesV in complex with ketimine intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: Y.59, L.60 Chain B: L.35 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: Y.59, L.60 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain C: R.58, Y.59, L.60 Chain D: L.35 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: L.35 Chain D: Y.59, L.60 Ligand excluded by PLIP

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

NA.2: 2 residues within 4Å: Chain A: N.85 Chain B: N.85 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.85 Water bridges: B:D.259 NA.11: 2 residues within 4Å: Chain C: N.85 Chain D: N.85 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.85

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

EDO.3: 7 residues within 4Å: Chain A: A.74, Y.75, E.77, R.192, R.197 Chain D: D.328, A.329 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.75, A:E.77, A:R.192, A:R.192, A:R.197 Water bridges: D:R.29 EDO.4: 8 residues within 4Å: Chain A: L.33, P.211, K.213, N.214, G.216, R.269, R.280, P.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.216, A:R.280 Water bridges: A:N.214, A:G.216 EDO.7: 8 residues within 4Å: Chain B: L.33, L.35, P.211, K.213, N.214, G.216, R.269, P.375 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.216, B:R.269 Water bridges: B:R.280, B:R.280 EDO.8: 4 residues within 4Å: Chain B: R.192, R.197, D.274, D.307 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.192, B:R.197, B:R.197, B:D.274 Water bridges: B:D.307, B:D.307 EDO.12: 2 residues within 4Å: Chain A: R.244 Chain C: H.80 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.80 Water bridges: C:R.236

4 x PGU: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid(Non-covalent)

PGU.5: 17 residues within 4Å: Chain A: S.86, G.87, M.88, Y.113, A.115, D.184, A.186, Q.187, S.208, Y.210, K.213, G.221, Y.338 Chain B: Y.241, Y.247, N.255, R.257 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.113, A:Y.113, A:A.115, A:A.186, A:Q.187, A:Y.210 Hydrogen bonds: A:G.87, A:M.88, A:Q.187, A:S.208, A:S.208, A:K.213, A:Y.338, A:Y.338, B:Y.241, B:Y.247, B:N.255 Water bridges: A:Y.210 Salt bridges: A:K.213, B:R.257 PGU.9: 19 residues within 4Å: Chain A: Y.241, K.246, Y.247, N.255, R.257 Chain B: S.86, G.87, M.88, Y.113, A.115, V.158, D.184, A.186, Q.187, S.208, Y.210, K.213, G.221, Y.338 23 PLIP interactions: 5 interactions with chain A, 18 interactions with chain B Hydrogen bonds: A:Y.241, A:N.255, B:G.87, B:M.88, B:Q.187, B:S.208, B:S.208, B:K.213, B:Y.338, B:Y.338 Salt bridges: A:K.246, A:K.246, A:R.257, B:K.213 Hydrophobic interactions: B:Y.113, B:Y.113, B:A.115, B:V.158, B:A.186, B:Q.187 Water bridges: B:Y.113, B:A.186, B:Y.210 PGU.13: 19 residues within 4Å: Chain C: S.86, G.87, M.88, Y.113, A.115, V.158, D.184, A.186, Q.187, S.208, Y.210, K.213, G.221, Y.338 Chain D: Y.241, K.246, Y.247, N.255, R.257 22 PLIP interactions: 17 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:Y.113, C:A.115, C:V.158, C:A.186, C:Q.187, C:Y.210 Hydrogen bonds: C:G.87, C:M.88, C:Q.187, C:S.208, C:S.208, C:K.213, C:Y.338, C:Y.338, D:Y.241, D:N.255 Water bridges: C:Y.113, C:A.186, D:K.246 Salt bridges: C:K.213, D:K.246, D:R.257 PGU.15: 18 residues within 4Å: Chain C: Y.241, K.246, Y.247, N.255, R.257 Chain D: S.86, G.87, M.88, Y.113, A.115, D.184, A.186, Q.187, S.208, Y.210, K.213, G.221, Y.338 21 PLIP interactions: 16 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:Y.113, D:Y.113, D:A.115, D:A.186, D:Q.187, D:Y.210 Hydrogen bonds: D:G.87, D:M.88, D:Q.187, D:S.208, D:S.208, D:K.213, D:Y.338, D:Y.338, C:Y.241, C:Y.247, C:N.255 Water bridges: D:A.186 Salt bridges: D:K.213, C:K.246, C:R.257

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Transaminase

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