MolNFT v1 · #88678 · protein
Crystal structure of the hera hexameric DNA translocase from sulfolobus solfataricus bound to AMP-pnp
4D2I: “Crystal structure of the hera hexameric DNA translocase from sulfolobus solfataricus bound to AMP-pnp”. X-ray diffraction, 2 ligands (ANP, MG), 13 pockets (best druggability 0.76). MolNFT v1 #88678 on GenesisL1: 3D structure…
- PDB
- 4D2I
- Type
- protein
- Length
- 922 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hera
- UniProt
- Q97WG8
- Ligands
- ANP, MG
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hera | protein | 464 | 36% helix, 22% strand | Q97WG8 |
| B | Hera | protein | 458 | 36% helix, 23% strand | Q97WG8 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.76 | 0.82 | 62 | empty |
| 2 | 373 | 0.62 | 0.78 | 38 | empty |
| 3 | 324 | 0.59 | 0.77 | 35 | empty |
| 4 | 242 | 0.53 | 0.77 | 32 | ANP, MG |
| 5 | 83 | 0.43 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3354 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4D2I · Crystal structure of the HerA hexameric DNA translocase from Sulfolobus solfataricus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q97WG8 · AlphaFold monomer V2.0 prediction for DNA double-strand break repair helicase hera… · a predicted model of the same protein · chain A 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 Q97WG8
- Elsewhere: RCSB PDB 4D2I · PDBe 4D2I · UniProt Q97WG8
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