MolNFT v1 · #175002 · protein + DNA

MAPE1-blunt-ended dsdna product complex

7CD5 · DNA(5'-D(*CP*GP*TP*AP*AP*TP*AP*CP*G)-3'): “MAPE1-blunt-ended dsdna product complex”. X-ray diffraction, 2 pockets (best druggability 0.57). MolNFT v1 #175002 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7CD5
Type: protein + DNA
Length: 286 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA(5'-D(*CP*GP*TP*AP*AP*TP*AP*CP*G)-3'); DNA-(apurinic or apyrimidinic site) endonuclease
EC: 3.1.-.-
UniProt: P28352
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	DNA(5'-D(CPGPTPAPAPTPAPCP*G)-3')	dna	8	—	—
A	DNA-(apurinic or apyrimidinic site) endonuclease (EC 3.1.-.-)	protein	278	29% helix, 25% strand	P28352

Pockets

2 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	196	0.57	0.80	29	empty
2	52	0.29	0.75	12	empty

Interfaces

1 interface between chains.

B–A · 267 Å² buried · 2 hydrogen bonds · protein-nucleic

Compared structures

7CD5 · mAPE1-blunt-ended dsDNA product complex · the same entry in another collection · chain B against B, TM-score 1.00
P28352 · AlphaFold monomer V2.0 prediction for DNA-(apurinic or apyrimidinic site) endonuclease… · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P28352
Elsewhere: RCSB PDB 7CD5 · PDBe 7CD5 · UniProt P28352

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