MolNFT v1 · #107058 · protein + DNA
Dead-box helicase MSS116 bound to ssdna and ADP-bef
4TYN · DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3'): “Dead-box helicase MSS116 bound to ssdna and ADP-bef”. X-ray diffraction, 3 ligands (BEF, ADP, MG), 3 pockets (best druggability 0.62). MolNFT v1 #107058 on GenesisL1: 3D structure, binding…
- PDB
- 4TYN
- Type
- protein + DNA
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3'); ATP-dependent RNA helicase MSS116, mitochondrial
- EC
- 3.6.4.13
- UniProt
- P15424
- Ligands
- BEF, ADP, MG
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3') | dna | 7 | — | — |
| A | ATP-dependent RNA helicase MSS116, mitochondrial (EC 3.6.4.13) | protein | 509 | 47% helix, 17% strand | P15424 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · chains A
- ADP · Adenosine-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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.62 | 0.79 | 54 | MG, BEF, ADP |
| 2 | 230 | 0.50 | 0.75 | 35 | empty |
| 3 | 72 | 0.36 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 943 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 4TYN · DEAD-box helicase Mss116 bound to ssDNA and ADP-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 4TYN · PDBe 4TYN · UniProt P15424
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