MolNFT v1 · #111365 · protein + DNA

Crystal structure of muty bound to its anti-substrate

4YOQ · A/G-specific adenine glycosylase: “Crystal structure of muty bound to its anti-substrate”. X-ray diffraction, 2 ligands (SF4, NA), 6 pockets (best druggability 0.72). MolNFT v1 #111365 on GenesisL1: 3D structure, binding sites and…

PDB: 4YOQ
Type: protein + DNA
Length: 365 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: A/G-specific adenine glycosylase; DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')…
EC: 3.2.2.-
UniProt: P83847
Ligands: SF4, NA
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	A/G-specific adenine glycosylase (EC 3.2.2.-)	protein	344	47% helix, 14% strand	P83847
B	DNA (5'-D(APAPGPAPCP(8OG)PTPGPGPAP*C)-3')	dna	11	—	—
C	DNA (5'-D(TGPTPCPCPAPCPGPTPCP*T)-3')	dna	10	—	—

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains A
NA · Sodium ion · metal · chains A, C
GOL · Glycerol · additive · chains A, B, C

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	389	0.72	0.84	48	empty
2	137	0.68	0.89	26	empty
3	569	0.66	0.77	44	GOL
4	156	0.53	0.81	25	empty
5	55	0.32	0.77	13	empty

Interfaces

3 interfaces between chains.

A–B · 896 Å² buried · 19 hydrogen bonds · protein-nucleic
A–C · 781 Å² buried · 22 hydrogen bonds · protein-nucleic
B–C · 415 Å² buried · 38 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

4YOQ · Crystal Structure of MutY bound to its anti-substrate · the same entry in another collection · chain A against A, TM-score 1.00
P83847 · AlphaFold monomer V2.0 prediction for adenine DNA glycosylase (P83847) · 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 P83847
Elsewhere: RCSB PDB 4YOQ · PDBe 4YOQ · UniProt P83847

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