Research workbench
Crystal structure of RABA1A in complex with gppnhp
Analyse Crystal structure of RABA1A in complex with gppnhp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XR6
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein RABA1A
- UniProt
- P28185
- Ligands
- GNP, MG
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RAS-related protein RABA1A | protein | 170 | 34% helix, 29% strand | P28185 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.68 | 0.77 | 76 | empty |
| 2 | 114 | 0.44 | 0.78 | 27 | GNP, MG |
| 3 | 101 | 0.40 | 0.77 | 24 | GNP, MG |
| 4 | 60 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 488 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 P28185
- Elsewhere: RCSB PDB 5XR6 · PDBe 5XR6 · UniProt P28185
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