Research workbench

PHF23 phd domain apo

Analyse PHF23 phd domain apo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WXK
Type: protein
Length: 248 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phd finger protein 23
UniProt: Q9BUL5
Ligands: ZN
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · 4 distinct chains · 2% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phd finger protein 23	protein	49	0% helix, 12% strand	Q9BUL5
B, C	Phd finger protein 23	protein	51	8% helix, 16% strand	Q9BUL5
D	Phd finger protein 23	protein	50	0% helix, 22% strand	Q9BUL5
E	Phd finger protein 23	protein	47	0% helix, 17% strand	Q9BUL5

Ligands and binding sites

ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E

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

Pockets

2 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	174	0.54	0.79	29	empty
2	138	0.45	0.77	20	empty

Interfaces

6 interfaces between chains.

B–C · 584 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 572 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 564 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 67 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 39 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6WXK · PHF23 PHD Domain Apo · the same entry in another collection · chain E against E, TM-score 1.00
Q9BUL5 · AlphaFold monomer V2.0 prediction for phd finger protein 23 (Q9BUL5) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 Q9BUL5
Elsewhere: RCSB PDB 6WXK · PDBe 6WXK · UniProt Q9BUL5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.