MolNFT v1 · #117533 · protein

Crystal structure of DNA2 nuclease-helicase

5EAW · DNA replication ATP-dependent HELICASE/NUCLEASE DNA2: “Crystal structure of DNA2 nuclease-helicase”. X-ray diffraction, 2 ligands (SF4, ADP), 20 pockets (best druggability 0.78). MolNFT v1 #117533 on GenesisL1: 3D structure, binding…

PDB: 5EAW
Type: protein
Length: 2,092 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA replication ATP-dependent HELICASE/NUCLEASE DNA2
EC: 3.1.-.-, 3.6.4.12
UniProt: Q6ZQJ5
Ligands: SF4, ADP
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA replication ATP-dependent HELICASE/NUCLEASE DNA2 (EC 3.1.-.-, 3.6.4.12)	protein	1046	40% helix, 20% strand	Q6ZQJ5

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	750	0.78	0.82	69	empty
2	127	0.78	0.96	26	empty
3	657	0.78	0.83	53	empty
4	133	0.78	0.95	29	empty
5	687	0.72	0.78	64	empty

Interfaces

1 interface between chains.

A–B · 1638 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

5EAW · Crystal structure of Dna2 nuclease-helicase · the same entry in another collection · chain A against A, TM-score 1.00
Q6ZQJ5 · AlphaFold monomer V2.0 prediction for DNA replication ATP-dependent HELICASE/NUCLEASE… · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q6ZQJ5
Elsewhere: RCSB PDB 5EAW · PDBe 5EAW · UniProt Q6ZQJ5

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