Research workbench
Crystal structure of the C3BOT-NAD-rala complex reveals a novel type of action of a bacterial exoenzyme
Analyse Crystal structure of the C3BOT-NAD-rala complex reveals a novel type of action… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A9K
- Type
- protein
- Length
- 377 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein ral-a; Mono-ADP-ribosyltransferase C3
- EC
- 2.4.2.-
- UniProt
- P11233, P15879
- Ligands
- GDP, NAD, MG
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein ral-a | protein | 170 | 42% helix, 25% strand | P11233 |
| B | Mono-ADP-ribosyltransferase C3 (EC 2.4.2.-) | protein | 207 | 37% helix, 26% strand | P15879 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains B
- 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.58 | 0.78 | 46 | NAD |
| 2 | 205 | 0.56 | 0.79 | 32 | MG, GDP |
Interfaces
1 interface between chains.
- A–B · 924 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2A9K · Crystal structure of the C3bot-NAD-RalA complex reveals a novel type of action of a… · the same entry in another collection · chain A against A, TM-score 1.00
- P11233 · AlphaFold monomer V2.0 prediction for RAS-related protein ral-a (P11233) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P11233
- Every structure of UniProt P15879
- Elsewhere: RCSB PDB 2A9K · PDBe 2A9K · UniProt P11233 · UniProt P15879
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