SMTL ID : 5vvt.1

Structural Investigations of the Substrate Specificity of Human O-GlcNAcase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x THR- LEU: ELK1 peptide(Non-covalent)

THR-LEU.1: 10 residues within 4Å: Chain A: Y.11, R.46, N.117, Y.161, F.165, V.196 Chain B: W.445, K.448, W.479 Ligands: NAG.3 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.11, A:F.165, A:V.196, B:W.445 Hydrogen bonds: A:Y.11, A:N.117, A:Y.161, A:Y.161 THR-LEU.2: 7 residues within 4Å: Chain A: W.445 Chain B: Y.11, L.83, N.117, D.119, Y.161 Ligands: NAG.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.11, B:L.83 Hydrogen bonds: B:Y.11, B:N.117, B:N.117, B:D.119, B:Y.161, B:Y.161

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.3: 13 residues within 4Å: Chain A: G.9, F.10, K.40, D.116, N.117, Y.161, V.196, W.220, N.222, D.227, Y.228, N.255 Ligands: THR-LEU.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.116, A:Y.161, A:W.220 Hydrogen bonds: A:G.9, A:K.40, A:K.40, A:D.116, A:N.117, A:N.222, A:D.227, A:N.255 NAG.4: 14 residues within 4Å: Chain B: G.9, F.10, Y.11, K.40, D.116, N.117, Y.161, V.196, W.220, N.222, D.227, Y.228, N.255 Ligands: THR-LEU-SER-PRO.2 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:D.116, B:Y.161, B:W.220 Hydrogen bonds: B:G.9, B:K.40, B:D.116, B:N.117, B:N.222, B:D.227, B:N.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, B. et al., Structural insights into the substrate binding adaptability and specificity of human O-GlcNAcase. Nat Commun (2017)

Release Date

2017-09-27

Peptides

Protein O-GlcNAcase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Protein O-GlcNAcase

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