MolNFT v1 · #75566 · protein

PHF2 jumonji-nog-FE(II) complex

3PU8 · Phd finger protein 2: “PHF2 jumonji-nog-FE(II) complex”. X-ray diffraction, 5 ligands (OGA, FE, SO4), 11 pockets (best druggability 0.77). MolNFT v1 #75566 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3PU8
Type: protein
Length: 728 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phd finger protein 2
UniProt: O75151
Ligands: OGA, FE, SO4, OXY, CL
Pockets: 11 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Phd finger protein 2	protein	365	43% helix, 21% strand	O75151
A	Phd finger protein 2	protein	363	41% helix, 21% strand	O75151

Ligands and binding sites

OGA · N-oxalylglycine · ligand · 2 copies · chains B, A
FE · Fe (III) ion · metal · 2 copies · chains B, A
SO4 · Sulfate ion · ion · 4 copies · chains B, A
OXY · Oxygen molecule · ion · 2 copies · chains B, A
CL · Chloride ion · ion · 2 copies · chains B, A
EDO · 1,2-ethanediol · additive · 18 copies · chains B, A

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

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	527	0.77	0.84	61	OXY, OGA, FE
2	627	0.76	0.82	63	OXY, OGA, FE
3	220	0.52	0.77	26	EDO, SO4
4	92	0.49	0.82	22	EDO, CL
5	109	0.48	0.80	22	EDO, CL

Interfaces

1 interface between chains.

B–A · 744 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3PU8 · PHF2 Jumonji-NOG-Fe(II) complex · 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 3PU8 · PDBe 3PU8 · UniProt O75151

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