SMTL ID : 7xpo.1

Crystal Structure of UDP-Glc/GlcNAc 4-Epimerase with NAD/UDP-Glc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 27 residues within 4Å: Chain A: G.13, G.16, Y.17, I.18, G.19, D.37, N.38, L.39, D.40, N.41, A.42, V.66, D.67, L.68, F.89, A.90, G.91, K.93, N.108, S.131, S.132, S.133, Y.157, K.161, Y.185, P.188 Ligands: UPG.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.185, A:P.188 Hydrogen bonds: A:Y.17, A:I.18, A:G.19, A:N.38, A:N.38, A:L.39, A:D.40, A:N.41, A:N.41, A:L.68, A:F.89, A:G.91, A:K.93, A:K.93, A:N.108, A:N.108, A:S.131, A:K.161 Water bridges: A:G.16, A:L.92, A:K.161, A:N.207 Salt bridges: A:K.93, A:K.93 NAD.5: 22 residues within 4Å: Chain B: G.13, G.16, Y.17, I.18, D.37, N.38, L.39, D.40, N.41, A.42, V.66, D.67, L.68, F.89, A.90, G.91, K.93, N.108, S.131, Y.157, K.161, Y.185 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:Y.17, B:I.18, B:G.19, B:N.38, B:N.38, B:L.39, B:D.40, B:N.41, B:N.41, B:L.68, B:F.89, B:G.91, B:N.108, B:N.108, B:S.131, B:Y.157, B:Y.157, B:K.161 Water bridges: B:G.16, B:L.92, B:K.93, B:K.161 Salt bridges: B:K.93, B:K.93

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

UPG.2: 20 residues within 4Å: Chain A: S.133, A.134, T.135, Y.185, F.186, N.187, N.206, N.207, L.208, L.223, T.224, V.225, Y.226, G.237, R.239, Y.241, V.280, R.303, D.306 Ligands: NAD.1 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.133, A:A.134, A:T.135, A:Y.185, A:N.187, A:N.206, A:N.207, A:N.207, A:L.208, A:T.224, A:Y.226, A:G.237 Water bridges: A:M.209, A:R.239, A:R.239, A:R.303, A:D.306 Salt bridges: A:R.239, A:R.303, A:R.303 pi-Stacking: A:Y.226 UPG.6: 19 residues within 4Å: Chain B: V.95, S.133, Y.157, F.186, N.187, P.188, N.207, L.208, Y.211, L.223, T.224, V.225, Y.226, G.237, R.239, Y.241, V.280, R.303, D.306 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.226 Hydrogen bonds: B:S.133, B:S.133, B:N.187, B:L.208, B:T.224, B:Y.226, B:Y.241, B:R.303 Water bridges: B:N.155, B:N.155, B:N.155, B:N.206, B:N.207, B:N.207, B:N.207, B:R.239, B:R.303, B:D.306, B:D.306, B:A.307 Salt bridges: B:R.239, B:R.303

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: R.7, Q.29, G.30, F.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.7, A:G.30 Water bridges: A:Q.29 GOL.4: 4 residues within 4Å: Chain A: L.27, Q.28, G.30, D.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.57 GOL.7: 2 residues within 4Å: Chain B: T.228, F.299 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.228 GOL.8: 4 residues within 4Å: Chain B: Q.25, V.245, K.326, Y.327 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.25, B:Y.327 Water bridges: B:Q.25, B:D.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Y. et al., A maize epimerase modulates cell wall synthesis and glycosylation during stomatal morphogenesis. Nat Commun (2023)

Release Date

2023-05-17

Peptides

UDP-glucose 4-epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UDP-glucose 4-epimerase

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