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
- 6RMC
- Type
- protein
- Length
- 1,375 residues
- Chains
- 4
- 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
- 16 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative mRNA splicing factor | protein | 642 | 44% helix, 19% strand | G0SEG4 |
| B | Putative mRNA splicing factor | protein | 645 | 45% helix, 19% strand | G0SEG4 |
| C, D | Putative pre-mRNA splicing protein | protein | 44 | 36% helix, 0% strand | G0SFN3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.83 | 0.84 | 121 | empty |
| 2 | 607 | 0.82 | 0.87 | 90 | empty |
| 3 | 156 | 0.79 | 0.95 | 21 | empty |
| 4 | 933 | 0.77 | 0.80 | 114 | empty |
| 5 | 129 | 0.69 | 0.90 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1781 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1779 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 550 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 542 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 338 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6RMC · 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 6RMC · PDBe 6RMC · UniProt G0SEG4 · UniProt G0SFN3
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