MolNFT v1 · #168325 · protein

Crystal structure of xenopus laevis APE2 catalytic domain

6WCD · DNA-(apurinic or apyrimidinic site) lyase: “Crystal structure of xenopus laevis APE2 catalytic domain”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.37). MolNFT v1 #168325 on GenesisL1: 3D structure, binding…

PDB: 6WCD
Type: protein
Length: 314 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-(apurinic or apyrimidinic site) lyase
EC: 4.2.99.18
UniProt: Q6DDT4
Ligands: MG
Pockets: 3 · best druggability 0.37

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18)	protein	314	28% helix, 26% strand	Q6DDT4

Ligands and binding sites

MG · Magnesium ion · metal · chains A
BU1 · 1,4-butanediol · additive · 3 copies · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
EDO · 1,2-ethanediol · additive · 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	53	0.37	0.80	15	empty
2	57	0.28	0.74	15	BU1
3	63	0.27	0.73	17	MG

Compared structures

6WCD · Crystal Structure of Xenopus laevis APE2 Catalytic Domain · the same entry in another collection · 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 Q6DDT4
Elsewhere: RCSB PDB 6WCD · PDBe 6WCD · UniProt Q6DDT4

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