MolNFT v1 · #135324 · protein

JMJD2A in complex with NI(II)

5TVS · Lysine-specific demethylase 4A: “JMJD2A in complex with NI(II)”. X-ray diffraction, 2 ligands (NI, ZN), 8 pockets (best druggability 0.73). MolNFT v1 #135324 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5TVS
Type: protein
Length: 696 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific demethylase 4A
EC: 1.14.11.-
UniProt: O75164
Ligands: NI, ZN
Pockets: 8 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lysine-specific demethylase 4A (EC 1.14.11.-)	protein	348	29% helix, 24% strand	O75164

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	801	0.73	0.78	73	empty
2	388	0.70	0.82	40	NI
3	343	0.69	0.83	41	NI
4	92	0.50	0.83	22	empty
5	94	0.38	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 419 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5TVS · JMJD2A in complex with Ni(II) · the same entry in another collection · chain A against A, TM-score 1.00

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 O75164
Elsewhere: RCSB PDB 5TVS · PDBe 5TVS · UniProt O75164

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