Research workbench
Crystal structure of the afadin RA1 domain in complex with HRAS
Analyse Crystal structure of the afadin RA1 domain in complex with HRAS in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AMB
- Type
- protein
- Length
- 249 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase HRAS; Afadin
- UniProt
- P01112, Q9QZQ1
- Ligands
- GNP, MG
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase HRAS | protein | 170 | 36% helix, 26% strand | P01112 |
| B | Afadin | protein | 79 | 22% helix, 39% strand | Q9QZQ1 |
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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.65 | 0.81 | 50 | GNP, MG |
| 2 | 82 | 0.35 | 0.75 | 19 | empty |
| 3 | 62 | 0.29 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 434 Ų buried · 7 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 P01112
- Every structure of UniProt Q9QZQ1
- Elsewhere: RCSB PDB 6AMB · PDBe 6AMB · UniProt P01112 · UniProt Q9QZQ1
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