MolNFT v1 · #111073 · protein + DNA

HUAB-20BP

4YFT · DNA-binding protein hu-beta: “HUAB-20BP”. X-ray diffraction, 2 pockets (best druggability 0.52). MolNFT v1 #111073 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YFT
Type: protein + DNA
Length: 167 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-binding protein hu-beta; Synthetic DNA strand; DNA-binding protein hu-alpha
UniProt: N4NVB4, P0ACF2
Pockets: 2 · best druggability 0.52

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-binding protein hu-beta	protein	76	47% helix, 21% strand	N4NVB4
B	Synthetic DNA strand	dna	9	—	—
D	Synthetic DNA strand	dna	11	—	—
C	DNA-binding protein hu-alpha	protein	71	54% helix, 23% strand	P0ACF2

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	347	0.52	0.73	29	empty
2	79	0.30	0.73	11	empty

Interfaces

4 interfaces between chains.

A–C · 1873 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 427 Å² buried · 38 hydrogen bonds · nucleic-nucleic
D–C · 247 Å² buried · 5 hydrogen bonds · protein-nucleic
A–B · 13 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

4YFT · HUab-20bp · the same entry in another collection · chain A against A, TM-score 1.00
P0ACF2 · AlphaFold monomer V2.0 prediction for DNA-binding protein hu-alpha (P0ACF2) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 N4NVB4
Every structure of UniProt P0ACF2
Elsewhere: RCSB PDB 4YFT · PDBe 4YFT · UniProt N4NVB4 · UniProt P0ACF2

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