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
- 6RM9
- Type
- protein
- Length
- 695 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
- Pockets
- 9 · best druggability 0.80
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 | 655 | 45% helix, 19% strand | G0SEG4 |
| C | Putative pre-mRNA splicing protein | protein | 40 | 28% helix, 0% strand | G0SFN3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.80 | 0.86 | 76 | ACT, GOL |
| 2 | 408 | 0.74 | 0.84 | 64 | ADP, MG, ACT |
| 3 | 204 | 0.69 | 0.87 | 38 | empty |
| 4 | 104 | 0.67 | 0.91 | 21 | empty |
| 5 | 93 | 0.59 | 0.87 | 23 | empty |
Interfaces
1 interface between chains.
- A–C · 1588 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6RM9 · 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 6RM9 · PDBe 6RM9 · UniProt G0SEG4 · UniProt G0SFN3
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