MolNFT v1 · #79016 · protein + RNA
Structure of MSS116P (nte and C-tail double deletion) bound to ssrna and AMP-pnp
3SQX · ATP-dependent RNA helicase MSS116, mitochondrial: “Structure of MSS116P (nte and C-tail double deletion) bound to ssrna and AMP-pnp”. X-ray diffraction, 2 ligands (ANP, MG), 5 pockets (best druggability 0.63). MolNFT v1 #79016 on…
- PDB
- 3SQX
- Type
- protein + RNA
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase MSS116, mitochondrial; RNA…
- EC
- 3.6.4.13
- UniProt
- P15424
- Ligands
- ANP, MG
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase MSS116, mitochondrial (EC 3.6.4.13) | protein | 508 | 46% helix, 16% strand | P15424 |
| B | RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') | rna | 6 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.63 | 0.81 | 34 | ANP, MG |
| 2 | 155 | 0.45 | 0.76 | 31 | empty |
| 3 | 63 | 0.38 | 0.79 | 15 | empty |
| 4 | 110 | 0.36 | 0.74 | 22 | empty |
| 5 | 69 | 0.30 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 745 Ų buried · 25 hydrogen bonds · protein-nucleic
Compared structures
- 3SQX · Structure of Mss116p (NTE and C-tail double deletion) bound to ssRNA and AMP-PNP · the same entry in another collection · chain A against A, TM-score 1.00
- P15424 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase MSS116, mitochondrial… · 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 P15424
- Elsewhere: RCSB PDB 3SQX · PDBe 3SQX · UniProt P15424
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