Research workbench
Dead-box helicase MSS116 bound to ssrna and ADP-bef
Analyse Dead-box helicase MSS116 bound to ssrna and ADP-bef in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TYW
- Type
- protein + RNA
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase MSS116, mitochondrial; RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')
- EC
- 3.6.4.13
- UniProt
- P15424
- Ligands
- BEF, ADP, MG
- Pockets
- 5 · best druggability 0.63
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, mitochondrial (EC 3.6.4.13) | protein | 508 | 45% helix, 17% strand | P15424 |
| B | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3') | rna | 7 | — | — |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · 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 | 269 | 0.63 | 0.81 | 49 | MG, BEF, ADP |
| 2 | 137 | 0.53 | 0.81 | 23 | empty |
| 3 | 194 | 0.48 | 0.76 | 27 | empty |
| 4 | 58 | 0.33 | 0.77 | 16 | empty |
| 5 | 52 | 0.26 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 846 Ų buried · 27 hydrogen bonds · protein-nucleic
Compared structures
- 4TYW · DEAD-box helicase Mss116 bound to ssRNA and ADP-BeF · 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 4TYW · PDBe 4TYW · UniProt P15424
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