MolNFT v1 · #136666 · protein + DNA

Crystal structure of human exonuclease 1 EXO1 (D173A) in complex with 5' recessed-end DNA (rv)

5V07: “Crystal structure of human exonuclease 1 EXO1 (D173A) in complex with 5' recessed-end DNA (rv)”. X-ray diffraction, 2 ligands (MN, NA), 6 pockets (best druggability 0.75). MolNFT v1 #136666 on GenesisL1: 3D structure, binding sites…

PDB: 5V07
Type: protein + DNA
Length: 367 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exonuclease 1; DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3'); DNA…
EC: 3.1.-.-
UniProt: Q9UQ84
Ligands: MN, NA
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Z	Exonuclease 1 (EC 3.1.-.-)	protein	344	51% helix, 13% strand	Q9UQ84
A	DNA (5'-D(CPGPCPTPAPGPTPCPGPAPCPAP*T)-3')	dna	13	—	—
B	DNA (5'-D(PTPCPGPAPCPTPAPGPCPG)-3')	dna	10	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains Z, B
NA · Sodium ion · metal · chains Z, A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	906	0.75	0.79	60	NA
2	126	0.52	0.81	18	MN
3	125	0.46	0.77	17	empty
4	135	0.45	0.77	18	empty
5	59	0.28	0.74	12	empty

Interfaces

3 interfaces between chains.

Z–A · 687 Å² buried · 16 hydrogen bonds · protein-nucleic
Z–B · 557 Å² buried · 17 hydrogen bonds · protein-nucleic
A–B · 463 Å² buried · 48 hydrogen bonds · nucleic-nucleic

Compared structures

5V07 · Crystal structure of human exonuclease 1 Exo1 (D173A) in complex with 5' recessed-end DNA… · the same entry in another collection · chain Z against Z, TM-score 1.00
Q9UQ84 · AlphaFold monomer V2.0 prediction for exonuclease 1 (Q9UQ84) · a predicted model of the same protein · chain Z 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 Q9UQ84
Elsewhere: RCSB PDB 5V07 · PDBe 5V07 · UniProt Q9UQ84

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