Research workbench
Dead-box helicase MSS116 bound to ssrna and cdp-bef
Analyse Dead-box helicase MSS116 bound to ssrna and cdp-bef in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TYY
- Type
- protein + RNA
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'); ATP-dependent RNA helicase MSS116…
- EC
- 3.6.4.13
- UniProt
- P15424
- Ligands
- BEF, CDP, MG
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | rna | 9 | — | — |
| A | ATP-dependent RNA helicase MSS116, mitochondrial (EC 3.6.4.13) | protein | 505 | 46% helix, 17% strand | P15424 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · chains A
- CDP · Cytidine-5'-diphosphate · 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 | 293 | 0.65 | 0.82 | 52 | BEF, CDP, MG |
| 2 | 247 | 0.52 | 0.76 | 39 | empty |
| 3 | 107 | 0.49 | 0.80 | 24 | empty |
| 4 | 102 | 0.37 | 0.76 | 16 | empty |
| 5 | 75 | 0.33 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 868 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 4TYY · DEAD-box helicase Mss116 bound to ssRNA and CDP-BeF · the same entry in another collection · chain B against B, 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 4TYY · PDBe 4TYY · UniProt P15424
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