MolNFT v1 · #113991 · protein

The crystal structure of SAUGI/HUMAN udg complex

5AYR · Uracil-DNA glycosylase: “The crystal structure of SAUGI/HUMAN udg complex”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.76). MolNFT v1 #113991 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5AYR
Type: protein
Length: 666 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uracil-DNA glycosylase; Uncharacterized protein
EC: 3.2.2.27
UniProt: P13051, Q936H5
Ligands: MG
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Uracil-DNA glycosylase (EC 3.2.2.27)	protein	224	39% helix, 11% strand	P13051
B, D	Uncharacterized protein	protein	109	27% helix, 39% strand	Q936H5

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1019	0.76	0.78	81	empty
2	60	0.37	0.78	13	empty
3	62	0.36	0.77	12	empty

Interfaces

5 interfaces between chains.

C–D · 1173 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1168 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 196 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 192 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 135 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5AYR · The crystal structure of SAUGI/human UDG complex · the same entry in another collection · chain A against A, TM-score 1.00
P13051 · AlphaFold monomer V2.0 prediction for uracil-DNA glycosylase (P13051) · 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 P13051
Every structure of UniProt Q936H5
Elsewhere: RCSB PDB 5AYR · PDBe 5AYR · UniProt P13051 · UniProt Q936H5

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