MolNFT v1 · #69599 · protein

Structure of KIAA1718 jumonji domain

3KV9 · Jmjc domain-containing histone demethylation protein 1D: “Structure of KIAA1718 jumonji domain”. X-ray diffraction, 2 ligands (FE2, OXY), 4 pockets (best druggability 0.74). MolNFT v1 #69599 on GenesisL1: 3D structure, binding sites…

PDB: 3KV9
Type: protein
Length: 366 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Jmjc domain-containing histone demethylation protein 1D
EC: 2.-.-.-
UniProt: Q6ZMT4
Ligands: FE2, OXY
Pockets: 4 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Jmjc domain-containing histone demethylation protein 1D (EC 2.-.-.-)	protein	366	42% helix, 22% strand	Q6ZMT4

Ligands and binding sites

FE2 · Fe (II) ion · metal · 2 copies · chains A
OXY · Oxygen molecule · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	472	0.74	0.83	47	FE2, OXY
2	52	0.37	0.80	20	empty
3	61	0.35	0.77	14	empty
4	73	0.33	0.75	19	empty

Compared structures

3KV9 · Structure of KIAA1718 Jumonji domain · the same entry in another collection · chain A against A, TM-score 1.00
Q6ZMT4 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 7A (Q6ZMT4) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q6ZMT4
Elsewhere: RCSB PDB 3KV9 · PDBe 3KV9 · UniProt Q6ZMT4

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