SMTL ID : 4gll.1

Crystal structure of human UDP-xylose synthase.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: G.12, A.14, G.15, F.16, V.17, D.36, N.37, F.38, F.39, T.40, G.41, H.60, D.61, V.62, L.76, A.77, S.78, P.79, A.80, T.95, A.117, S.118, T.119, Y.148, K.152, I.175, F.176, N.177, T.178, H.184 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.175 Hydrogen bonds: A:G.12, A:F.16, A:V.17, A:N.37, A:F.38, A:F.39, A:T.40, A:T.40, A:T.40, A:T.40, A:G.41, A:D.61, A:V.62, A:L.76, A:S.78, A:Y.148, A:K.152, A:T.178, A:T.178 Water bridges: A:G.15, A:G.18 Salt bridges: A:H.184 NAD.4: 32 residues within 4Å: Chain B: G.12, A.14, G.15, F.16, V.17, D.36, N.37, F.38, F.39, T.40, G.41, H.60, D.61, V.62, L.76, A.77, S.78, P.79, A.80, K.91, T.95, A.117, S.118, T.119, Y.148, K.152, I.175, F.176, N.177, T.178, H.184, R.189 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.175 Hydrogen bonds: B:F.16, B:V.17, B:G.18, B:N.37, B:N.37, B:F.39, B:T.40, B:T.40, B:T.40, B:G.41, B:D.61, B:V.62, B:L.76, B:S.78, B:P.79, B:K.91, B:Y.148, B:K.152, B:T.178, B:R.189, B:R.189 Salt bridges: B:H.184

2 x GAI: GUANIDINE(Non-covalent)

GAI.2: 6 residues within 4Å: Chain A: F.194, T.205, V.206, Y.207, I.248, D.273 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.205, A:T.205, A:Y.207 Salt bridges: A:D.273 pi-Cation interactions: A:Y.207 GAI.5: 7 residues within 4Å: Chain B: V.190, F.194, T.205, V.206, Y.207, I.248, D.273 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.205, B:T.205, B:Y.207 Salt bridges: B:D.273 pi-Cation interactions: B:Y.207

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: S.120, F.176, N.177, Q.276, R.278 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.120, A:N.177, A:N.177, A:Q.276 Salt bridges: A:R.278 SO4.6: 6 residues within 4Å: Chain B: Y.207, G.208, S.209, G.210, S.211, Q.212 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.209, B:G.210, B:S.211, B:S.211, B:Q.212, B:Q.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Polizzi, S.J. et al., Human UDP-alpha-d-xylose Synthase and Escherichia coli ArnA Conserve a Conformational Shunt That Controls Whether Xylose or 4-Keto-Xylose Is Produced. Biochemistry (2012)

Release Date

2012-09-05

Peptides

UDP-glucuronic acid decarboxylase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UDP-glucuronic acid decarboxylase 1