MolNFT v1 · #168042 · protein + DNA

APE1 exonuclease substrate complex D148E

6W3N · Tcgacggatcc: “APE1 exonuclease substrate complex D148E”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.75). MolNFT v1 #168042 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6W3N
Type: protein + DNA
Length: 593 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tcgacggatcc; DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(C7R))-3'); Ggatccgtcgatcgcatcagc…
EC: 3.1.-.-, 4.2.99.18
UniProt: P27695
Ligands: CA
Pockets: 9 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Tcgacggatcc	dna	11	—	—
D	DNA (5'-D(GPCPTPGPAPTPGPCPGP(C7R))-3')	dna	9	—	—
E	Ggatccgtcgatcgcatcagc	dna	21	—	—
A, B	DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18)	protein	276	29% helix, 25% strand	P27695

Ligands and binding sites

CA · Calcium ion · metal · chains D
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	299	0.75	0.88	34	empty
2	306	0.56	0.76	29	empty
3	243	0.55	0.77	36	empty
4	150	0.45	0.76	31	empty
5	114	0.43	0.77	21	empty

Interfaces

6 interfaces between chains.

E–B · 551 Å² buried · 6 hydrogen bonds · protein-nucleic
A–B · 503 Å² buried · 4 hydrogen bonds · protein-protein
C–E · 475 Å² buried · 34 hydrogen bonds · nucleic-nucleic
D–E · 423 Å² buried · 43 hydrogen bonds · nucleic-nucleic
D–B · 328 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

6W3N · APE1 exonuclease substrate complex D148E · the same entry in another collection · chain D against D, 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 B 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 P27695
Elsewhere: RCSB PDB 6W3N · PDBe 6W3N · UniProt P27695

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