MolNFT v1 · #121489 · protein

APOBEC3F catalytic domain crystal structure

5HX5 · DNA dc->du-editing enzyme apobec-3F: “APOBEC3F catalytic domain crystal structure”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.67). MolNFT v1 #121489 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5HX5
Type: protein
Length: 342 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA dc->du-editing enzyme apobec-3F
EC: 3.5.4.-
UniProt: Q8IUX4
Ligands: ZN
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA dc->du-editing enzyme apobec-3F (EC 3.5.4.-)	protein	174	43% helix, 25% strand	Q8IUX4
B	DNA dc->du-editing enzyme apobec-3F (EC 3.5.4.-)	protein	168	42% helix, 24% strand	Q8IUX4

Ligands and binding sites

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

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	605	0.67	0.77	58	empty
2	84	0.42	0.79	19	empty
3	80	0.37	0.77	16	empty
4	88	0.35	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 403 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5HX5 · APOBEC3F Catalytic Domain Crystal Structure · the same entry in another collection · chain A against A, TM-score 1.00
Q8IUX4 · AlphaFold monomer V2.0 prediction for DNA dc->du-editing enzyme apobec-3F (Q8IUX4) · 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 Q8IUX4
Elsewhere: RCSB PDB 5HX5 · PDBe 5HX5 · UniProt Q8IUX4

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