SMTL ID : 6cbo.1 (1 other biounit)

X-ray structure of GenB1 from micromonospora echinospora in complex with neamine and PLP (as the external aldimine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.1: 9 residues within 4Å: Chain A: G.30, L.33, A.34, Q.35, E.36, P.37, R.41, P.47 Chain B: W.103 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:E.276, A:G.30 Salt bridges: A:R.41 MPO.4: 9 residues within 4Å: Chain A: W.103 Chain B: G.30, L.33, A.34, Q.35, E.36, P.37, R.41, P.47 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.33 Salt bridges: B:E.36, B:R.41 Water bridges: A:E.276

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

EDO.2: 1 residues within 4Å: Chain A: S.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.147, A:S.147 EDO.5: 7 residues within 4Å: Chain B: R.144, R.146, P.191, E.192, V.194, A.221, D.222 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.144, B:R.144, B:R.146, B:P.191, B:D.222

2 x DOW: (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2-amino-2,6-dideoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-alpha-D-glucopyranoside(Non-covalent)

DOW.3: 22 residues within 4Å: Chain A: T.38, R.73, T.128, G.129, T.130, Y.154, H.155, G.156, S.200, D.228, V.230, K.231, K.254, F.364, D.367, N.368, G.414, A.415, D.417 Chain B: S.279, F.280, T.281 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.230 Hydrogen bonds: A:G.129, A:T.130, A:K.231, A:K.254, A:K.254, A:K.254, A:K.254, A:N.368, A:D.417, A:D.417, B:S.279, B:S.279, B:T.281, B:T.281 Water bridges: A:Y.154, A:Y.154, B:S.282 pi-Stacking: A:Y.154 DOW.6: 22 residues within 4Å: Chain A: S.279, F.280, T.281 Chain B: T.38, R.73, T.128, G.129, T.130, Y.154, H.155, G.156, S.200, D.228, V.230, K.231, K.254, F.364, D.367, N.368, G.414, A.415, D.417 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.230 Hydrogen bonds: B:T.38, B:G.129, B:T.130, B:K.254, B:K.254, B:K.254, B:K.254, B:N.368, B:D.417, B:D.417, A:S.279, A:T.281, A:T.281 Water bridges: B:Y.157, B:K.254, B:N.368, B:D.417, A:S.282 pi-Stacking: B:Y.154

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

C-6' aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C-6' aminotransferase

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