MolNFT v1 · #66957 · protein + RNA
Structure of MSS116P bound to ssrna and ADP-beryllium fluoride
3I61 · ATP-dependent RNA helicase MSS116: “Structure of MSS116P bound to ssrna and ADP-beryllium fluoride”. X-ray diffraction, 3 ligands (ADP, BEF, MG), 5 pockets (best druggability 0.64). MolNFT v1 #66957 on GenesisL1: 3D structure…
- PDB
- 3I61
- 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*UP*UP*UP*UP*UP*UP*U)-3'
- EC
- 3.6.1.-
- UniProt
- P15424
- Ligands
- ADP, BEF, MG
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase MSS116 (EC 3.6.1.-) | protein | 509 | 45% helix, 17% strand | P15424 |
| B | 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3' | rna | 10 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- BEF · Beryllium trifluoride ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.64 | 0.79 | 52 | ADP, BEF, MG |
| 2 | 212 | 0.51 | 0.77 | 37 | empty |
| 3 | 54 | 0.33 | 0.78 | 13 | empty |
| 4 | 70 | 0.30 | 0.73 | 21 | empty |
| 5 | 56 | 0.27 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1164 Ų buried · 33 hydrogen bonds · protein-nucleic
Compared structures
- 3I61 · Structure of Mss116p bound to ssRNA and ADP-Beryllium Fluoride · 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 3I61 · PDBe 3I61 · UniProt P15424
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