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Crystal structure of the RNA-helicase PRP43 from chaetomium thermophilum bound to ADP
Analyse Crystal structure of the RNA-helicase PRP43 from chaetomium thermophilum bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D0U
- Type
- protein
- Length
- 705 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
- UniProt
- G0RY84
- Ligands
- ADP, MG
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 | protein | 705 | 44% helix, 18% strand | G0RY84 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.84 | 0.84 | 120 | DMS |
| 2 | 365 | 0.67 | 0.81 | 47 | ADP, MG |
| 3 | 206 | 0.53 | 0.78 | 27 | DMS |
| 4 | 53 | 0.40 | 0.81 | 14 | DMS |
| 5 | 70 | 0.40 | 0.79 | 16 | empty |
Compared structures
- 5D0U · Crystal structure of the RNA-helicase Prp43 from Chaetomium thermophilum bound to ADP · the same entry in another collection · 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 G0RY84
- Elsewhere: RCSB PDB 5D0U · PDBe 5D0U · UniProt G0RY84
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