MolNFT v1 · #75553 · protein

PHF2 jumonji domain

3PTR · Phd finger protein 2: “PHF2 jumonji domain”. X-ray diffraction, 5 pockets (best druggability 0.75). MolNFT v1 #75553 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3PTR
Type: protein
Length: 366 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phd finger protein 2
UniProt: O75151
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Phd finger protein 2	protein	366	41% helix, 20% strand	O75151

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 19 copies · chains B

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

Pockets

5 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	419	0.75	0.85	52	EDO
2	83	0.49	0.82	21	empty
3	67	0.37	0.78	18	EDO
4	64	0.32	0.75	18	empty
5	60	0.31	0.75	16	empty

Compared structures

3PTR · PHF2 Jumonji domain · the same entry in another collection · chain B against B, TM-score 1.00
O75151 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase PHF2 (O75151) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 O75151
Elsewhere: RCSB PDB 3PTR · PDBe 3PTR · UniProt O75151

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