SMTL ID : 5xoo.1

The structure of hydra Fam20 with sugar

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-dimer

Ligands

1 x XYP- GAL: beta-D-galactopyranose-(1-4)-beta-D-xylopyranose(Non-covalent)

XYP-GAL.1: 11 residues within 4Å: Chain A: T.92, Q.93, Y.126, E.127, G.128, Y.129, Y.192, D.277, H.279, K.299 Ligands: MBN.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.93, A:Y.126, A:E.127, A:G.128, A:K.299, A:T.92, A:Q.93, A:D.277, A:H.279, A:K.299 Salt bridges: A:H.279

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 1 residues within 4Å: Chain A: N.203 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: N.286, E.287, N.288 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.287 NAG.6: 2 residues within 4Å: Chain B: N.203, V.204 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.204 NAG.7: 2 residues within 4Å: Chain B: E.287, N.288 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.287, B:E.287

1 x MBN: TOLUENE(Non-covalent)

MBN.4: 4 residues within 4Å: Chain A: Y.231, H.279, H.280 Ligands: XYP-GAL.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.231, A:Y.231 pi-Stacking: A:H.279

2 x ADN: ADENOSINE(Non-covalent)

ADN.5: 7 residues within 4Å: Chain A: Y.89, L.212, W.213, L.214, K.222, E.282, L.295 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.212, A:L.214, A:K.222, A:E.282 pi-Stacking: A:W.213 ADN.8: 6 residues within 4Å: Chain B: L.212, W.213, L.214, V.220, E.282, L.295 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.212, B:L.214, B:E.282 pi-Stacking: B:W.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., Structure and evolution of the Fam20 kinases. Nat Commun (2018)

Release Date

2018-04-11

Peptides

Glycosaminoglycan xylosylkinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycosaminoglycan xylosylkinase

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