MolNFT v1 · #66954 · protein + RNA
Structure of MSS116P bound to ssrna containing a single 5-bru and AMP- pnp
3I5Y · ATP-dependent RNA helicase MSS116: “Structure of MSS116P bound to ssrna containing a single 5-bru and AMP- pnp”. X-ray diffraction, 2 ligands (ANP, MG), 7 pockets (best druggability 0.65). MolNFT v1 #66954 on GenesisL1: 3D…
- PDB
- 3I5Y
- Type
- protein + RNA
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase MSS116; 5'-R(*UP*UP*UP*(5BU)P*UP*UP*UP*UP*UP*U)-3'
- EC
- 3.6.1.-
- UniProt
- P15424
- Ligands
- ANP, MG
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase MSS116 (EC 3.6.1.-) | protein | 509 | 46% helix, 17% strand | P15424 |
| B | 5'-R(*UP*UP*UP*(5BU)P*UP*UP*UP*UP*UP*U)-3' | rna | 10 | — | — |
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
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.65 | 0.79 | 58 | ANP, MG |
| 2 | 136 | 0.39 | 0.74 | 33 | empty |
| 3 | 50 | 0.37 | 0.80 | 11 | empty |
| 4 | 54 | 0.36 | 0.79 | 12 | empty |
| 5 | 64 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1130 Ų buried · 32 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3I5Y · Structure of Mss116p bound to ssRNA containing a single 5-BrU 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 3I5Y · PDBe 3I5Y · UniProt P15424
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