SMTL ID : 5w70.1

X-ray Structure of RbmB from Streptomyces ribosidificus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x 9YM: [4-({[(1R,2S,3S,4R,5S)-5-amino-2,3,4-trihydroxycyclohexyl]amino}methyl)-5-hydroxy-6-methylpyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)

9YM.1: 20 residues within 4Å: Chain A: S.96, G.97, T.98, L.101, S.122, W.123, A.125, V.168, D.194, A.196, Q.197, S.218, Q.220, K.223, G.230, Y.367 Chain B: S.65, R.252, M.264, N.276 19 PLIP interactions: 12 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:W.123, A:V.168, A:A.196 Hydrogen bonds: A:G.97, A:T.98, A:T.98, A:Q.197, A:S.218, A:K.223, B:S.65, B:S.65, B:R.252, B:R.252, B:N.276 Water bridges: A:Q.220, A:Y.367, A:Y.367, B:D.250, B:N.276 9YM.2: 18 residues within 4Å: Chain A: S.65, R.252, M.264, N.276 Chain B: S.96, G.97, T.98, L.101, S.122, W.123, V.168, D.194, A.196, Q.197, S.218, Q.220, K.223, Y.332 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:W.123, B:V.168 Hydrogen bonds: B:G.97, B:T.98, B:T.98, B:Q.197, B:S.218, B:K.223, A:S.65, A:S.65, A:R.252, A:R.252, A:N.276 Water bridges: B:Y.332, A:N.276

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

EDO.3: 2 residues within 4Å: Chain B: F.399, E.405 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.399

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zachman-Brockmeyer, T.R. et al., The structure of RbmB from Streptomyces ribosidificus, an aminotransferase involved in the biosynthesis of ribostamycin. Protein Sci. (2017)

Release Date

2017-07-12

Peptides

L-glutamine:2-deoxy-scyllo-inosose aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

L-glutamine:2-deoxy-scyllo-inosose aminotransferase