Research workbench
Crystal structure of the rpgr RCC1-like domain in complex with the rpgr-interacting domain of RPGRIP1
Analyse Crystal structure of the rpgr RCC1-like domain in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QAM
- Type
- protein
- Length
- 544 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- X-linked retinitis pigmentosa GTPase regulator; X-linked retinitis pigmentosa GTPase…
- UniProt
- Q92834, Q96KN7
- Ligands
- MG
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | X-linked retinitis pigmentosa GTPase regulator | protein | 364 | 6% helix, 46% strand | Q92834 |
| B | X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 | protein | 180 | 23% helix, 36% strand | Q96KN7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.77 | 0.89 | 45 | GOL |
| 2 | 239 | 0.55 | 0.77 | 40 | empty |
| 3 | 54 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1298 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 4QAM · Crystal Structure of the RPGR RCC1-like domain in complex with the RPGR-interacting… · 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
- Q96KN7 · AlphaFold monomer V2.0 prediction for X-linked retinitis pigmentosa GTPase… · a predicted model of the same protein · chain B against A, TM-score 0.96
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
- Every structure of UniProt Q96KN7
- Elsewhere: RCSB PDB 4QAM · PDBe 4QAM · UniProt Q92834 · UniProt Q96KN7
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