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
- 6RMA
- Type
- protein
- Length
- 688 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, CL
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative mRNA splicing factor | protein | 654 | 45% helix, 19% strand | G0SEG4 |
| B | Putative pre-mRNA splicing protein | protein | 34 | 21% helix, 0% strand | G0SFN3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- IPA · Isopropyl alcohol · additive · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.85 | 0.86 | 125 | CL, GOL |
| 2 | 371 | 0.66 | 0.80 | 43 | ADP, MG |
| 3 | 98 | 0.63 | 0.89 | 21 | empty |
| 4 | 190 | 0.47 | 0.75 | 28 | empty |
| 5 | 99 | 0.46 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1536 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6RMA · 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 6RMA · PDBe 6RMA · UniProt G0SEG4 · UniProt G0SFN3
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