SMTL ID : 5vvu.1

Structural Investigations of the Substrate Specificity of Human O-GlcNAcase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x PRO- TYR- SER- SER: TAB1 peptide(Non-covalent)

PRO-TYR-SER-SER.1: 12 residues within 4Å: Chain A: Y.11, N.117, I.118, Y.161, F.165, V.196 Chain B: F.425, T.426, W.445, K.448, W.479 Ligands: NAG.3 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.425, B:W.445 Hydrogen bonds: B:K.448, B:K.448, A:N.117, A:Y.161 PRO-TYR-SER-SER.2: 10 residues within 4Å: Chain A: F.425, S.429, W.445 Chain B: Y.11, R.46, N.117, Y.161, F.165, V.196 Ligands: NAG.4 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.425, A:W.445, B:Y.11 Hydrogen bonds: A:S.429, B:Y.11, B:R.46, B:R.46, B:N.117, B:Y.161

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

NAG.3: 16 residues within 4Å: Chain A: G.9, F.10, Y.11, K.40, D.116, N.117, Y.161, T.192, V.196, W.220, N.222, A.225, D.227, Y.228, N.255 Ligands: PRO-TYR-SER-SER.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:D.116, A:Y.161 Hydrogen bonds: A:G.9, A:K.40, A:K.40, A:D.116, A:N.222, A:D.227, A:N.255 NAG.4: 16 residues within 4Å: Chain B: G.9, F.10, Y.11, K.40, D.116, N.117, C.157, Y.161, V.196, W.220, N.222, A.225, D.227, Y.228, N.255 Ligands: PRO-TYR-SER-SER.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:K.40, B:D.116, 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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