Structure of PDB 5vmz Chain A

Receptor sequence

>5vmzA (length=122) Species: 9606 (Homo sapiens)

DDHYELIVDGRVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKV
FPLAQYRTKHEIHHTGERRYQCLACGKSFINYQFMSSHIKSVHSQDPSGD
SKLYRLHPCRSLQIRQYAYLSD

3D structure

• PDB: 5vmz CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso.
• Chain: A
• Resolution: 2.319 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	R501 Y503 V504 C505 S508 R511 Q535 Y536 Q563 F564 R595 Y597 A598	R21 Y23 V24 C25 S28 R31 Q55 Y56 Q83 F84 R115 Y117 A118	PDBbind-CN: Kd=7.2nM
BS02	dna	A	R511 K520 Y522 A534 Q535 T538 R549 Y550 Y562 S578 G579 Y584 L586 R595 Y597	R31 K40 Y42 A54 Q55 T58 R69 Y70 Y82 S98 G99 Y104 L106 R115 Y117	PDBbind-CN: Kd=7.2nM
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:5vmz, PDBe:5vmz, PDBj:5vmz
• PDBsum: 5vmz
• PubMed: 29546986
• UniProt: Q86T24|KAISO_HUMAN Transcriptional regulator Kaiso (Gene Name=ZBTB33)