Research workbench
The crystal structure of the rpgr RCC1-like domain in complex with PDE6D
Analyse The crystal structure of the rpgr RCC1-like domain in complex with PDE6D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JHP
- Type
- protein
- Length
- 504 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta…
- UniProt
- O43924, Q92834
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta | protein | 142 | 13% helix, 61% strand | O43924 |
| C | X-linked retinitis pigmentosa GTPase regulator | protein | 362 | 5% helix, 45% strand | Q92834 |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.83 | 0.91 | 44 | empty |
| 2 | 270 | 0.78 | 0.90 | 45 | empty |
| 3 | 540 | 0.71 | 0.80 | 95 | empty |
Interfaces
1 interface between chains.
- B–C · 951 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4JHP · The crystal structure of the RPGR RCC1-like domain in complex with PDE6D · the same entry in another collection · chain B against B, TM-score 1.00
- O43924 · AlphaFold monomer V2.0 prediction for retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q92834 · AlphaFold monomer V2.0 prediction for X-linked retinitis pigmentosa GTPase regulator… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 O43924
- Every structure of UniProt Q92834
- Elsewhere: RCSB PDB 4JHP · PDBe 4JHP · UniProt O43924 · UniProt Q92834
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