Research workbench
Structure of human RAB8A in complex with the bmerb domain of mical-cl
Analyse Structure of human RAB8A in complex with the bmerb domain of mical-cl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SZI
- Type
- protein
- Length
- 314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-8A; Mical C-terminal-like protein
- UniProt
- P61006, Q6ZW33
- Ligands
- GNP, MG
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-8A | protein | 174 | 37% helix, 26% strand | P61006 |
| B | Mical C-terminal-like protein | protein | 140 | 90% helix, 0% strand | Q6ZW33 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.75 | 0.78 | 72 | GNP, MG |
| 2 | 64 | 0.42 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 854 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5SZI · Structure of human Rab8a in complex with the bMERB domain of Mical-cL · the same entry in another collection · chain A against A, TM-score 1.00
- P61006 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-8A (P61006) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P61006
- Every structure of UniProt Q6ZW33
- Elsewhere: RCSB PDB 5SZI · PDBe 5SZI · UniProt P61006 · UniProt Q6ZW33
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