MolNFT v1 · #128855 · protein
A structure of the gef kalirin DH1 domain in complex with the small GTPase RAC1
5O33 · RAS-related C3 botulinum toxin substrate 1: “A structure of the gef kalirin DH1 domain in complex with the small GTPase RAC1”. X-ray diffraction, 1 ligand (GDP), 3 pockets (best druggability 0.53). MolNFT v1 #128855 on GenesisL1: 3D…
- PDB
- 5O33
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related C3 botulinum toxin substrate 1; Kalirin
- EC
- 2.7.11.1
- UniProt
- P63000, P97924
- Ligands
- GDP
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related C3 botulinum toxin substrate 1 | protein | 177 | 37% helix, 23% strand | P63000 |
| B | Kalirin (EC 2.7.11.1) | protein | 179 | 77% helix, 0% strand | P97924 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
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 | 211 | 0.53 | 0.77 | 28 | GDP |
| 2 | 205 | 0.53 | 0.78 | 32 | empty |
| 3 | 62 | 0.30 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1270 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5O33 · A structure of the GEF Kalirin DH1 domain in complex with the small GTPase Rac1 · the same entry in another collection · 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 P63000
- Every structure of UniProt P97924
- Elsewhere: RCSB PDB 5O33 · PDBe 5O33 · UniProt P63000 · UniProt P97924
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