Research workbench
Crystal structure of DNA2 in complex with a 5' overhang DNA
Analyse Crystal structure of DNA2 in complex with a 5' overhang DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EAN
- Type
- protein + DNA
- Length
- 1,066 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication ATP-dependent HELICASE/NUCLEASE DNA2; DNA…
- EC
- 3.1.-.-, 3.6.4.12
- UniProt
- Q6ZQJ5
- Ligands
- SF4, ADP, CA
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA replication ATP-dependent HELICASE/NUCLEASE DNA2 (EC 3.1.-.-, 3.6.4.12) | protein | 1051 | 40% helix, 22% strand | Q6ZQJ5 |
| B | DNA (5'-D(P*AP*CP*TP*CP*TP*GP*CP*CP*AP*AP*GP*AP*GP*GP*A)- 3') | dna | 15 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.88 | 0.90 | 70 | CA |
| 2 | 564 | 0.84 | 0.89 | 66 | empty |
| 3 | 403 | 0.83 | 0.91 | 62 | empty |
| 4 | 97 | 0.58 | 0.87 | 28 | empty |
| 5 | 162 | 0.52 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2049 Ų buried · 36 hydrogen bonds · protein-nucleic
Compared structures
- 5EAN · Crystal structure of Dna2 in complex with a 5' overhang DNA · 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 A 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 5EAN · PDBe 5EAN · UniProt Q6ZQJ5
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