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Structure of the mouse 8-oxoguanine DNA glycosylase MOGG1 in complex with ligand TH9525

Analyse Structure of the mouse 8-oxoguanine DNA glycosylase MOGG1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6G40
Type: protein
Length: 947 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N-GLYCOSYLASE/DNA lyase
EC: 3.2.2.-, 4.2.99.18
UniProt: O08760
Ligands: ELK, NI
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18)	protein	316	49% helix, 11% strand	O08760
C	N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18)	protein	315	47% helix, 11% strand	O08760

Ligands and binding sites

ELK · ~{N}-(3-methoxy-4-methyl-phenyl)-4-(4-methoxy-2-oxidanylidene-3~{H}-benzimidazol-1-yl)piperidine-1-carboxamide · ligand · 3 copies · chains A, C, B
NI · Nickel (II) ion · metal · chains A, B, C
ACT · Acetate ion · additive · 4 copies · chains A, B, C
PEG · Di(hydroxyethyl)ether · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	816	0.77	0.81	86	ELK, ACT
2	612	0.74	0.81	61	PEG, ELK
3	374	0.71	0.83	44	ELK
4	54	0.58	0.91	17	empty
5	51	0.52	0.89	17	empty

Interfaces

3 interfaces between chains.

A–B · 507 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 376 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 314 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6G40 · Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH9525 · the same entry in another collection · chain A against A, TM-score 1.00
O08760 · AlphaFold monomer V2.0 prediction for N-GLYCOSYLASE/DNA lyase (O08760) · a predicted model of the same protein · chain A 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 O08760
Elsewhere: RCSB PDB 6G40 · PDBe 6G40 · UniProt O08760

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