MolNFT v1 · #158977 · protein + DNA

HUAE34K 19BP sym DNA

6OAJ · DNA-binding protein hu-alpha: “HUAE34K 19BP sym DNA”. X-ray diffraction, 3 pockets (best druggability 0.80). MolNFT v1 #158977 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6OAJ
Type: protein + DNA
Length: 335 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-binding protein hu-alpha; DNA (5'- D(P*CP*GP*GP*TP*TP*CP*AP*AP*TP*TP*GP*GP*CP*AP*CP*GP…
UniProt: P0ACF0
Pockets: 3 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 48% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-binding protein hu-alpha	protein	71	49% helix, 17% strand	P0ACF0
B	DNA-binding protein hu-alpha	protein	79	44% helix, 24% strand	P0ACF0
C	DNA-binding protein hu-alpha	protein	76	47% helix, 22% strand	P0ACF0
D	DNA-binding protein hu-alpha	protein	70	51% helix, 21% strand	P0ACF0
K	DNA (5'- D(PCPGPGPTPTPCPAPAPTPTPGPGPCPAPCPGPCPGP*C)-3')	dna	19	—	—
L	DNA (5'- D(PGPCPGPCPGPTPGPCPCPAPAPTPTPGPAPAPCPCPGPC)-3')	dna	20	—	—

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1145	0.80	0.81	72	empty
2	56	0.72	0.97	18	empty
3	91	0.36	0.75	11	empty

Interfaces

14 interfaces between chains.

C–D · 1756 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 1744 Å² buried · 4 hydrogen bonds · protein-protein
K–L · 826 Å² buried · 58 hydrogen bonds · nucleic-nucleic
C–K · 235 Å² buried · 5 hydrogen bonds · protein-nucleic
C–L · 170 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

6OAJ · HUaE34K 19bp SYM DNA · the same entry in another collection · chain L against L, TM-score 1.00
P0ACF0 · AlphaFold monomer V2.0 prediction for DNA-binding protein hu-alpha (P0ACF0) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 P0ACF0
Elsewhere: RCSB PDB 6OAJ · PDBe 6OAJ · UniProt P0ACF0

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