Research workbench
Crystal structure of RAS-related C3 botulinum toxin substrate 1 isoform X2 from naegleria fowleri in complex with GDP
Analyse Crystal structure of RAS-related C3 botulinum toxin substrate 1 isoform X2 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VCU
- Type
- protein
- Length
- 370 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related C3 botulinum toxin substrate 1 isoform X2
- Ligands
- GDP, MG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related C3 botulinum toxin substrate 1 isoform X2 | protein | 186 | 41% helix, 22% strand | — |
| B | RAS-related C3 botulinum toxin substrate 1 isoform X2 | protein | 184 | 41% helix, 23% strand | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.72 | 0.80 | 63 | empty |
| 2 | 116 | 0.45 | 0.78 | 27 | GDP, MG |
| 3 | 92 | 0.38 | 0.76 | 28 | GDP, MG |
| 4 | 56 | 0.31 | 0.76 | 18 | empty |
| 5 | 55 | 0.28 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 756 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5VCU · Crystal structure of ras-related c3 botulinum toxin substrate 1 isoform x2 from Naegleria… · 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
- Elsewhere: RCSB PDB 5VCU · PDBe 5VCU
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