MolNFT v1 · #136667 · protein + DNA

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

5V08: “Crystal structure of human exonuclease 1 EXO1 (D173A) in complex with 5' recessed-end DNA (rvi)”. X-ray diffraction, 2 ligands (MG, NA), 6 pockets (best druggability 0.76). MolNFT v1 #136667 on GenesisL1: 3D structure, binding sites…

PDB: 5V08
Type: protein + DNA
Length: 366 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: MG, NA
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Z	Exonuclease 1 (EC 3.1.-.-)	protein	343	50% 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

MG · Magnesium ion · metal · 3 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	924	0.76	0.79	71	MG
2	131	0.54	0.82	22	MG
3	150	0.47	0.78	19	empty
4	122	0.45	0.77	16	empty
5	52	0.27	0.74	12	empty

Interfaces

3 interfaces between chains.

Z–A · 703 Å² buried · 11 hydrogen bonds · protein-nucleic
Z–B · 555 Å² buried · 12 hydrogen bonds · protein-nucleic
A–B · 473 Å² buried · 54 hydrogen bonds · nucleic-nucleic

Compared structures

5V08 · 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 5V08 · PDBe 5V08 · UniProt Q9UQ84

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