MolNFT v2 · #162752 · protein
Crystal structure of DEAH-box ATPase Prp43-S387A
6QID: “Crystal structure of DEAH-box ATPase Prp43-S387A”. X-ray diffraction at 2.204, 5 ligands (ADP, BEF, MG), 7 pockets (best druggability 0.72). MolNFT v2 #162752 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6QID
- Type
- protein
- Length
- 703 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.204
- Source
- Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
- Molecule
- Prp43
- UniProt
- G0RY84
- Ligands
- ADP, BEF, MG, CL, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.204 · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prp43 | protein | 703 | 45% helix, 18% strand | G0RY84 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- BEF · Beryllium trifluoride ion · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 5 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 11 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.72 | 0.76 | 80 | MPD, CL, SO4 |
| 2 | 399 | 0.68 | 0.80 | 39 | MPD |
| 3 | 225 | 0.64 | 0.83 | 36 | MG, ADP, BEF |
| 4 | 165 | 0.62 | 0.84 | 34 | empty |
| 5 | 72 | 0.35 | 0.76 | 16 | MPD |
Compared structures
- 6QID · Crystal structure of deah-box ATPase PRP43-S387A · 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 6QID · PDBe 6QID · UniProt G0RY84
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