SMTL ID : 6cbn.1

x-ray structure of NeoB from streptomyces fradiae in complex with PLP and neomycin (as the external aldimine) at pH 7.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x OZY: (1R,2R,3S,4R,6S)-4,6-diamino-2-[(3-O-{2-amino-2,6-dideoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-alpha-D-glucopyranosyl}-beta-D-ribofuranosyl)oxy]-3-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside(Non-covalent)

OZY.1: 24 residues within 4Å: Chain A: T.35, R.70, S.125, G.126, T.127, Y.151, H.152, G.153, S.198, D.226, V.228, K.229, K.253, Y.363, D.366, N.367, N.413, V.414, D.416 Chain B: K.275, E.276, S.278, F.279, T.280 27 PLIP interactions: 18 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:Y.151, A:V.228 Hydrogen bonds: A:T.35, A:G.126, A:T.127, A:K.229, A:K.253, A:K.253, A:D.366, A:N.367, A:N.413, A:D.416, B:E.276, B:E.276, B:T.280, B:T.280 Water bridges: A:T.35, A:K.253, A:Y.363, A:Y.363, A:D.416, A:D.416, B:K.275, B:E.276, B:E.276, B:E.276, B:S.281 OZY.3: 24 residues within 4Å: Chain A: K.275, E.276, F.279, T.280 Chain B: F.33, T.35, R.70, S.125, G.126, T.127, Y.151, H.152, G.153, S.198, D.226, V.228, K.229, K.253, Y.363, D.366, N.367, N.413, V.414, D.416 28 PLIP interactions: 22 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.151, B:V.228 Hydrogen bonds: B:T.35, B:T.35, B:G.126, B:T.127, B:T.127, B:K.229, B:K.253, B:K.253, B:Y.363, B:D.366, B:N.367, B:N.413, B:N.413, B:D.416, A:K.275, A:E.276, A:T.280, A:T.280 Water bridges: B:R.70, B:Y.151, B:Y.151, B:K.253, B:D.416, A:S.278, A:S.281 Salt bridges: B:R.70

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

EDO.2: 8 residues within 4Å: Chain A: R.124, S.125, A.128, Y.154 Chain B: R.124, S.125, A.128, Y.154 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.125, B:S.125, B:Y.154, A:S.125, A:S.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dow, G.T. et al., The three-dimensional structure of NeoB: An aminotransferase involved in the biosynthesis of neomycin. Protein Sci. (2018)

Release Date

2018-02-21

Peptides

Neamine transaminase NeoN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Neamine transaminase NeoN

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