Structure of PDB 6dqb Chain A

Receptor sequence

>6dqbA (length=295) Species: 9606 (Homo sapiens) [Search protein sequence]

AEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPP
FACEVKSFRFTPRVQRLNELEAMAVREYTLQSFGEMADNFKSDYFNMPVH
MVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILP
EEEEYALSGWNLNNMPVLEQSVLKVPWLYVGMCFSSFCWHIEDHWSYSIN
YLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPN
VLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT

3D structure

PDB

6dqb Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A.

Chain

Resolution

1.791 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1)	Y179 H190 E192 H278 A290
Enzyme Commision number	1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.

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	H77	A	R73 Y409 A411 D412 W470 Y472 F480 C481 H483 K501 W503 Q535 L536 H571	R63 Y126 A128 D129 W177 Y179 F187 C188 H190 K208 W210 Q242 L243 H278
BS02	HZV	A	R73 Y409 D412 W470 Y472 F480 C481 H483 K501 W503 H571	R63 Y126 D129 W177 Y179 F187 C188 H190 K208 W210 H278
BS03	HZM	A	R73 Y409 A411 D412 Y472 F480 C481 H483 K501 W503 H571	R63 Y126 A128 D129 Y179 F187 C188 H190 K208 W210 H278	PDBbind-CN: -logKd/Ki=6.49,IC50=0.32uM
BS04	MN	A	H483 E485 H571	H190 E192 H278

External links

PDB	RCSB:6dqb, PDBe:6dqb, PDBj:6dqb
PDBsum	6dqb
PubMed	30392349
UniProt	P29375\|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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