Structure of PDB 5d9y Chain A

Receptor sequence

>5d9yA (length=413) Species: 9606 (Homo sapiens)

SCRCVEQIIEKDEGPFYTHLGAGPNVAAIREIMEERFGQKGKAIRIERVI
YTGKEGKSSQGCPIAKWVVRRSSSEEKLLCLVRERAGHTCEAAVIVILIL
VWEGIPLSLADKLYSELTETLRKYGTLTNRRCALNEERTCACQGLDPETC
GASFSFGCSWSMYYNGCKFARSKIPRKFKLLGDDPKEEEKLESHLQNLST
LMAPTYKKLAPDAYNNQIEYEHRAPECRLGLKEGRPFSGVTACLDFCAHA
HRDLHNMQNGSTLVCTLTREDNREFGGKPEDEQLHVLPLYKVSDVDEFGS
VEAQEEKKRSGAIQVLSSFRRKVRMLAEPVKTCGSDEVWSDSEQSFLDPD
IGGVAVAPTHGSILIECAKRELHATTPLKNPNRNHPTRISLVFYQHKSMN
EPKHGLALWEAKM

3D structure

• PDB: 5d9y Structural insight into substrate preference for TET-mediated oxidation.
• Chain: A
• Resolution: 1.971 Å

Enzymatic activity

• Enzyme Commision number: 1.14.11.80: methylcytosine dioxygenase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	R1261 R1262 S1286 S1290 M1293 Y1294 K1299 R1302 S1303 T1372 T1463 Y1902 H1904	R130 R131 S155 S159 M162 Y163 K168 R171 S172 T241 T332 Y394 H396	PDBbind-CN: Kd=0.9uM
BS02	dna	A	M1293 Y1294 N1296	M162 Y163 N165	PDBbind-CN: Kd=0.9uM
BS03	FE	A	H1382 D1384 H1881	H251 D253 H373
BS04	ZN	A	C1135 H1219 C1221	C4 H88 C90
BS05	ZN	A	C1193 C1271 C1273 H1380	C62 C140 C142 H249
BS06	ZN	A	C1289 C1298 C1358 H1912	C158 C167 C227 H404

Gene Ontology

Molecular Function

• GO:0070579 5-methylcytosine dioxygenase activity

Biological Process

• GO:0141166 chromosomal 5-methylcytosine DNA demethylation pathway

External links

• PDB: RCSB:5d9y, PDBe:5d9y, PDBj:5d9y
• PDBsum: 5d9y
• PubMed: 26524525
• UniProt: Q6N021|TET2_HUMAN Methylcytosine dioxygenase TET2 (Gene Name=TET2)