MolNFT v1 · #136669 · protein + DNA

Crystal structure of human exonuclease 1 EXO1 (D225A) in complex with 5' recessed-end DNA (rviii)

5V0A: “Crystal structure of human exonuclease 1 EXO1 (D225A) in complex with 5' recessed-end DNA (rviii)”. X-ray diffraction, 3 ligands (DA, MN, NA), 3 pockets (best druggability 0.79). MolNFT v1 #136669 on GenesisL1: 3D structure, binding…

PDB: 5V0A
Type: protein + DNA
Length: 368 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*TP*CP*AP*T)-3'); DNA…
EC: 3.1.-.-
UniProt: Q9UQ84
Ligands: DA, MN, NA
Pockets: 3 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Z	Exonuclease 1 (EC 3.1.-.-)	protein	346	49% helix, 13% strand	Q9UQ84
A	DNA (5'-D(CPGPCPTPAPGPTPCPGPTPCPAP*T)-3')	dna	13	—	—
B	DNA (5'-D(PCPGPAPCPTPAPGPCP*G)-3')	dna	9	—	—

Ligands and binding sites

DA · 2'-deoxyadenosine-5'-monophosphate · ligand · chains Z, A, B
MN · Manganese (II) ion · metal · 6 copies · chains Z, B, A
NA · Sodium ion · metal · chains Z, 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1016	0.79	0.81	79	MN, DA
2	106	0.33	0.73	18	empty
3	58	0.28	0.74	16	empty

Interfaces

3 interfaces between chains.

Z–A · 699 Å² buried · 15 hydrogen bonds · protein-nucleic
A–B · 435 Å² buried · 40 hydrogen bonds · nucleic-nucleic
Z–B · 343 Å² buried · 16 hydrogen bonds · protein-nucleic

Compared structures

5V0A · Crystal structure of human exonuclease 1 Exo1 (D225A) in complex with 5' recessed-end DNA… · the same entry in another collection · chain B against B, 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 5V0A · PDBe 5V0A · UniProt Q9UQ84

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