Research workbench
The holostructure of the branched-chain keto acid decarboxylase (kdca) from lactococcus lactis
Analyse The holostructure of the branched-chain keto acid decarboxylase (kdca) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VBF
- Type
- protein
- Length
- 1,092 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Branched-chain alpha-ketoacid decarboxylase
- UniProt
- Q6QBS4
- Ligands
- TPP, MG
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Branched-chain alpha-ketoacid decarboxylase | protein | 546 | 42% helix, 18% strand | Q6QBS4 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.84 | 0.97 | 48 | MG, TPP |
| 2 | 182 | 0.81 | 0.96 | 42 | MG, TPP |
| 3 | 399 | 0.63 | 0.77 | 38 | empty |
| 4 | 347 | 0.62 | 0.78 | 36 | empty |
| 5 | 167 | 0.45 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3485 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 2VBF · The holostructure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus… · 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 Q6QBS4
- Elsewhere: RCSB PDB 2VBF · PDBe 2VBF · UniProt Q6QBS4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.