Research workbench

HUaa 19bp SYM DNA pH 5.5

Analyse HUaa 19bp SYM DNA pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6O6K
Type: protein + DNA
Length: 166 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.601
Source: Escherichia coli (strain K12); SYNTHETIC CONSTRUCT
Molecule: DNA-binding protein HU-alpha; DNA (5'-D(P*AP*TP*TP*TP*CP*AP*TP*GP*AP*T)-3'); DNA…
UniProt: P0ACF2
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · resolution 3.601 · 4 distinct chains · 51% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-binding protein HU-alpha	protein	77	48% helix, 19% strand	P0ACF2
B	DNA-binding protein HU-alpha	protein	69	54% helix, 22% strand	P0ACF2
C	DNA (5'-D(PAPTPTPTPCPAPTPGPAPT)-3')	dna	10	—	—
D	DNA (5'-D(PCPAPTPCPAPTPGPAPAPA)-3')	dna	10	—	—

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	120	0.45	0.79	16	empty
2	115	0.37	0.74	17	empty

Interfaces

5 interfaces between chains.

A–B · 1859 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 399 Å² buried · 23 hydrogen bonds · nucleic-nucleic
B–C · 212 Å² buried · 3 hydrogen bonds · protein-nucleic
A–D · 168 Å² buried · 3 hydrogen bonds · protein-nucleic
B–D · 58 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

6O6K · Huaa 19BP sym DNA pH 5.5 · 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 B against A, TM-score 0.98

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 P0ACF2
Elsewhere: RCSB PDB 6O6K · PDBe 6O6K · UniProt P0ACF2

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