MolNFT v1 · #104660 · protein

Crystal structure of MG2+ bound human APE1

4QHE · DNA-(apurinic or apyrimidinic site) lyase: “Crystal structure of MG2+ bound human APE1”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.38). MolNFT v1 #104660 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4QHE
Type: protein
Length: 281 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-(apurinic or apyrimidinic site) lyase
EC: 3.1.-.-, 4.2.99.18
UniProt: P27695
Ligands: MG
Pockets: 3 · best druggability 0.38

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18)	protein	281	28% helix, 25% strand	P27695

Ligands and binding sites

MG · Magnesium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 6 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	107	0.38	0.75	17	empty
2	69	0.36	0.77	16	empty
3	65	0.32	0.76	16	empty

Compared structures

4QHE · Crystal structure of Mg2+ bound human APE1 · the same entry in another collection · chain A against A, TM-score 1.00
P27695 · 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 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 P27695
Elsewhere: RCSB PDB 4QHE · PDBe 4QHE · UniProt P27695

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