Structure of PDB 2ydr Chain A Binding Site BS01

Receptor Information

>2ydr Chain A (length=579) Species: 1502 (Clostridium perfringens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

QVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTAN
NIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSND
GKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFY
GTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRM
QELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGV
RSFAIYWDNIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITVPTEYDTGA
MVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYDR
NMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKI
SIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKT
WAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNL
KANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEI
AQNKLNTALSSFAVISEKVAQSFIQEALS

Ligand information

>2ydr Chain P (length=8) Species: 9606 (Homo sapiens) [Search peptide sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

LWVDSTPP

Receptor-Ligand Complex Structure

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Structure summary

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PDB	2ydr Synergy of Peptide and Sugar in O-Glcnacase Substrate Recognition.
Resolution	2.75 Å
Binding residue (original residue number in PDB)	Y189 N298 Y402 W490
Binding residue (residue number reindexed from 1)	Y150 N259 Y363 W451

Enzymatic activity

Enzyme Commision number

3.2.1.169: protein O-GlcNAcase.

External links

PDB	RCSB:2ydr, PDBe:2ydr, PDBj:2ydr
PDBsum	2ydr
PubMed	22365600
UniProt	Q0TR53\|OGA_CLOP1 O-GlcNAcase NagJ (Gene Name=nagJ)

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