Research workbench
The crystal structure of the rpgr RCC1-like domain
Analyse The crystal structure of the rpgr RCC1-like domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JHN
- Type
- protein
- Length
- 1,443 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- X-linked retinitis pigmentosa GTPase regulator
- UniProt
- Q92834
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | X-linked retinitis pigmentosa GTPase regulator | protein | 361 | 4% helix, 47% strand | Q92834 |
| C | X-linked retinitis pigmentosa GTPase regulator | protein | 361 | 5% helix, 46% strand | Q92834 |
| D | X-linked retinitis pigmentosa GTPase regulator | protein | 360 | 5% helix, 47% strand | Q92834 |
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.88 | 0.89 | 121 | empty |
| 2 | 745 | 0.86 | 0.89 | 102 | empty |
| 3 | 301 | 0.76 | 0.88 | 48 | empty |
| 4 | 270 | 0.76 | 0.89 | 46 | empty |
| 5 | 73 | 0.67 | 0.94 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–D · 762 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 698 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 96 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 28 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JHN · The crystal structure of the RPGR RCC1-like domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q92834 · AlphaFold monomer V2.0 prediction for X-linked retinitis pigmentosa GTPase regulator… · a predicted model of the same protein · 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 Q92834
- Elsewhere: RCSB PDB 4JHN · PDBe 4JHN · UniProt Q92834
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