Research workbench

HOGG1 borohydride-trapped intermediate without 8-oxoguanine

Analyse HOGG1 borohydride-trapped intermediate without 8-oxoguanine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1LWY
Type: protein + DNA
Length: 344 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'- D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'; 5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED)…
EC: 3.2.2.-
UniProt: O15527
Pockets: 6 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	5'- D(GPGPTPAPGPAPCPCPTPGPGPAPCPGP*C)-3'	dna	15	—	—
E	5'-D(GPCPGPTPCPCPAP(PED) PGPTPCPTPAPCP*C)-3'	dna	15	—	—
A	8-oxoguanine DNA glycosylase (EC 3.2.2.-)	protein	314	47% helix, 12% strand	O15527

Pockets

6 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	55	0.73	0.99	21	empty
2	445	0.61	0.76	43	empty
3	87	0.46	0.81	17	empty
4	118	0.43	0.77	21	empty
5	92	0.30	0.72	15	empty

Interfaces

3 interfaces between chains.

E–A · 646 Å² buried · 22 hydrogen bonds · protein-nucleic
D–E · 634 Å² buried · 63 hydrogen bonds · nucleic-nucleic
D–A · 434 Å² buried · 15 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

1LWY · hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine · the same entry in another collection · chain D against D, TM-score 1.00
O15527 · AlphaFold monomer V2.0 prediction for N-GLYCOSYLASE/DNA lyase (O15527) · a predicted model of the same protein · chain A 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 O15527
Elsewhere: RCSB PDB 1LWY · PDBe 1LWY · UniProt O15527

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