Research workbench
Crystal structure of DNA2 in complex with an ssdna
Analyse Crystal structure of DNA2 in complex with an ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EAX
- Type
- protein + DNA
- Length
- 2,126 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication ATP-dependent HELICASE/NUCLEASE DNA2; DNA (5'…
- EC
- 3.1.-.-, 3.6.4.12
- UniProt
- Q6ZQJ5
- Ligands
- SF4, ADP
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 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 |
| E, H | DNA (5'- D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 17 | — | — |
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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.86 | 0.88 | 84 | empty |
| 2 | 541 | 0.85 | 0.91 | 50 | empty |
| 3 | 635 | 0.85 | 0.89 | 57 | empty |
| 4 | 564 | 0.83 | 0.89 | 61 | empty |
| 5 | 838 | 0.81 | 0.84 | 92 | empty |
Interfaces
3 interfaces between chains.
- A–E · 2147 Ų buried · 35 hydrogen bonds · protein-nucleic
- B–H · 2127 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–B · 1689 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5EAX · Crystal structure of Dna2 in complex with an ssDNA · 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 5EAX · PDBe 5EAX · UniProt Q6ZQJ5
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