Structure of PDB 5vmu Chain A

Receptor sequence

>5vmuA (length=121) Species: 9606 (Homo sapiens)

DDHYELIVDGRVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKV
FPLAEYRTKHEIHHTGERRYQCLACGKSFINYQFMSSHIKSVHSQDPSGD
SKLYRLHPCRSLQIRQYAYLS

3D structure

• PDB: 5vmu CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso.
• Chain: A
• Resolution: 2.346 Å

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	Y503 V504 S508 R511 E535 Y536 Q563 F564 Y597 A598	Y23 V24 S28 R31 E55 Y56 Q83 F84 Y117 A118	PDBbind-CN: Kd=0.2nM
BS02	dna	A	R511 Y522 E535 T538 R549 Y550 Y562 G579 Y584 L586 R595 Y597 Y599	R31 Y42 E55 T58 R69 Y70 Y82 G99 Y104 L106 R115 Y117 Y119	PDBbind-CN: Kd=0.2nM
BS03	ZN	A	C496 C499 H512 H516	C16 C19 H32 H36
BS04	ZN	A	C524 C527 H540 H544	C44 C47 H60 H64
BS05	ZN	A	C552 C555 H568 H573	C72 C75 H88 H93

External links

• PDB: RCSB:5vmu, PDBe:5vmu, PDBj:5vmu
• PDBsum: 5vmu
• PubMed: 29546986
• UniProt: Q86T24|KAISO_HUMAN Transcriptional regulator Kaiso (Gene Name=ZBTB33)