MolNFT v1 · #84568 · protein

Structure of bsudg-P56 complex

3ZOQ · Uracil-DNA glycosylase: “Structure of bsudg-P56 complex”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.63). MolNFT v1 #84568 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3ZOQ
Type: protein
Length: 324 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uracil-DNA glycosylase; P56
EC: 3.2.2.27
UniProt: P39615, Q38503
Ligands: CL
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uracil-DNA glycosylase (EC 3.2.2.27)	protein	223	40% helix, 10% strand	P39615
B	P56	protein	48	19% helix, 54% strand	Q38503
C	P56	protein	53	19% helix, 49% strand	Q38503

Ligands and binding sites

CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · chains A, B

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

Pockets

4 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	92	0.63	0.89	28	GOL, CL
2	102	0.44	0.78	16	empty
3	122	0.40	0.75	20	empty
4	83	0.37	0.76	14	empty

Interfaces

3 interfaces between chains.

A–B · 851 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 698 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 205 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

3ZOQ · Structure of BsUDG-p56 complex · the same entry in another collection · chain A against A, TM-score 1.00
P39615 · AlphaFold monomer V2.0 prediction for uracil-DNA glycosylase (P39615) · 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 P39615
Every structure of UniProt Q38503
Elsewhere: RCSB PDB 3ZOQ · PDBe 3ZOQ · UniProt P39615 · UniProt Q38503

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