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Exonuclease X in complex with 3' overhanging duplex DNA

Analyse Exonuclease X in complex with 3' overhanging duplex DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FZX
Type: protein + DNA
Length: 366 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(P*GP*TP*CP*AP*TP*TP*GP*TP*GP*GP*AP*TP*CP*CP*GP*AP*G)-3'); DNA (5'…
EC: 3.1.11.-
UniProt: P0AEK0
Ligands: NA
Pockets: 2 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	DNA (5'- D(PGPTPCPAPTPTPGPTPGPGPAPTPCPCPGPAP*G)-3')	dna	17	—	—
A	DNA (5'- D(PCPGPGPAPTPCPCPAPCPAPAPTPGPAPCPCP*T)-3')	dna	17	—	—
C, D	Exodeoxyribonuclease 10 (EC 3.1.11.-)	protein	166	41% helix, 21% strand	P0AEK0

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains B, C, A, D

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

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	220	0.61	0.82	28	empty
2	98	0.39	0.77	16	empty

Interfaces

5 interfaces between chains.

B–A · 672 Å² buried · 66 hydrogen bonds · nucleic-nucleic
A–D · 595 Å² buried · 7 hydrogen bonds · protein-nucleic
B–C · 565 Å² buried · 9 hydrogen bonds · protein-nucleic
B–D · 281 Å² buried · 5 hydrogen bonds · protein-nucleic
A–C · 146 Å² buried · 2 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

4FZX · Exonuclease X in complex with 3' overhanging duplex DNA · the same entry in another collection · chain B against B, TM-score 1.00
P0AEK0 · AlphaFold monomer V2.0 prediction for exodeoxyribonuclease 10 (P0AEK0) · a predicted model of the same protein · chain C 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 P0AEK0
Elsewhere: RCSB PDB 4FZX · PDBe 4FZX · UniProt P0AEK0

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