Research workbench
Crystal structure of the deah-box ATPase PRP2 in complex with SPP2 and ADP
Analyse Crystal structure of the deah-box ATPase PRP2 in complex with SPP2 and ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RM8
- Type
- protein
- Length
- 700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative mRNA splicing factor; Putative pre-mRNA splicing protein
- UniProt
- G0SEG4, G0SFN3
- Ligands
- ADP, MG, SO4, CL
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative mRNA splicing factor | protein | 655 | 44% helix, 18% strand | G0SEG4 |
| C | Putative pre-mRNA splicing protein | protein | 45 | 29% helix, 0% strand | G0SFN3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 9 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.83 | 0.86 | 93 | SO4, CL, PEG |
| 2 | 311 | 0.70 | 0.84 | 42 | ADP, MG |
| 3 | 114 | 0.62 | 0.87 | 21 | SO4 |
| 4 | 233 | 0.56 | 0.78 | 30 | empty |
| 5 | 63 | 0.52 | 0.86 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 1687 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6RM8 · Crystal structure of the DEAH-box ATPase Prp2 in complex with Spp2 and 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 G0SEG4
- Every structure of UniProt G0SFN3
- Elsewhere: RCSB PDB 6RM8 · PDBe 6RM8 · UniProt G0SEG4 · UniProt G0SFN3
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