SMTL ID : 6h0n.1

The structure of wild-type Arabidopsis thaliana UDP-apiose/UDP-xylose synthase in complex with NAD+ and UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.02 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 24 residues within 4Å: Chain A: G.24, G.26, G.27, F.28, I.29, D.49, V.50, I.75, N.76, I.77, L.96, A.97, A.98, C.100, F.137, S.138, T.139, Y.185, K.189, P.212, N.214, W.215, R.235 Ligands: PO4.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.212 Hydrogen bonds: A:G.26, A:F.28, A:I.29, A:G.30, A:V.50, A:N.76, A:I.77, A:K.78, A:L.96, A:A.98, A:K.189, A:W.215, A:W.215, A:R.235, A:R.235 Salt bridges: A:R.235 NAD.4: 25 residues within 4Å: Chain B: G.24, G.26, G.27, F.28, I.29, D.49, V.50, I.75, N.76, I.77, K.78, L.96, A.97, A.98, C.100, F.137, S.138, T.139, Y.185, K.189, P.212, N.214, W.215, R.235 Ligands: PO4.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:P.212 Hydrogen bonds: B:G.26, B:F.28, B:I.29, B:G.30, B:V.50, B:N.76, B:I.77, B:K.78, B:L.96, B:A.98, B:Y.185, B:K.189, B:W.215 Salt bridges: B:R.235

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

UDP.2: 19 residues within 4Å: Chain A: P.102, E.141, R.182, N.214, R.235, V.236, C.239, F.240, K.251, L.252, V.253, R.260, V.298, F.330, Y.331, Y.335, D.337, R.341 Ligands: PO4.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.236 Hydrogen bonds: A:E.141, A:N.214, A:V.236, A:K.251, A:V.253, A:Y.335, A:Y.335, A:D.337 Salt bridges: A:R.182, A:R.260, A:R.341 UDP.5: 19 residues within 4Å: Chain B: P.102, E.141, R.182, N.214, R.235, V.236, C.239, F.240, K.251, L.252, V.253, R.260, V.298, F.330, Y.331, Y.335, D.337, R.341 Ligands: PO4.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.236, B:F.330 Hydrogen bonds: B:V.236, B:K.251, B:V.253, B:Y.331, B:Y.331, B:Y.335, B:D.337 Salt bridges: B:R.182, B:R.260, B:R.341

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 10 residues within 4Å: Chain A: C.100, P.102, Y.105, T.139, E.141, Y.185, R.235, R.341 Ligands: NAD.1, UDP.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:C.100, A:Y.105, A:Y.105, A:T.139, A:T.139, A:E.141, A:Y.185, A:R.235, A:R.341 PO4.6: 10 residues within 4Å: Chain B: C.100, P.102, Y.105, T.139, E.141, Y.185, R.235, R.341 Ligands: NAD.4, UDP.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.105, B:T.139, B:Y.185, B:R.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Savino, S. et al., Deciphering the enzymatic mechanism of sugar ring contraction in UDP-apiose biosynthesis. Nat Catal (2019)

Release Date

2019-10-23

Peptides

UDP-D-apiose/UDP-D-xylose synthase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UDP-D-apiose/UDP-D-xylose synthase 1