SMTL ID : 7vm0.1

Crystal structure of YojK from B.subtilis in complex with UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 19 residues within 4Å: Chain A: E.12, G.13, N.16, R.217, S.237, G.239, T.240, I.241, S.266, Y.288, V.289, Q.291, H.304, G.306, M.307, N.308, S.309, E.312 Ligands: GOL.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:N.16, A:R.217, A:R.217, A:T.240, A:I.241, A:S.266, A:V.289, A:V.289, A:Q.291, A:Q.291, A:N.308, A:N.308, A:S.309, A:E.312 Water bridges: A:G.13, A:G.268, A:G.268, A:Y.288, A:H.304, A:E.312, A:Q.329, A:Q.329 Salt bridges: A:H.304, A:H.304 UDP.4: 19 residues within 4Å: Chain B: E.12, G.13, N.16, R.217, S.237, G.239, T.240, I.241, S.266, Y.288, V.289, Q.291, H.304, G.306, M.307, N.308, S.309, E.312 Ligands: GOL.5 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:N.16, B:R.217, B:R.217, B:T.240, B:I.241, B:S.266, B:V.289, B:V.289, B:Q.291, B:Q.291, B:N.308, B:N.308, B:S.309, B:E.312 Water bridges: B:G.13, B:G.13, B:M.238, B:G.268, B:H.304, B:E.312, B:Q.329 Salt bridges: B:H.304, B:H.304

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: T.129, T.130, G.306, M.307, D.328 Ligands: UDP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.307, A:D.328 Water bridges: A:N.308, A:Q.329 GOL.3: 5 residues within 4Å: Chain A: T.67, N.244, Q.245, K.246, Q.247 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.244, A:N.244, A:K.246, A:Q.247 Water bridges: A:F.248 GOL.5: 7 residues within 4Å: Chain B: G.13, H.14, T.130, M.307, N.308, D.328 Ligands: UDP.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.308, B:D.328 Water bridges: B:G.13, B:Q.329

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 1 residues within 4Å: Chain B: E.151 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.151, B:E.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, B. et al., Highly efficient production of rebaudioside D enabled by structure-guided engineering of bacterial glycosyltransferase YojK. Front Bioeng Biotechnol (2022)

Release Date

2022-10-12

Peptides

Glycosyl transferase family 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycosyl transferase family 1