Research workbench
The complex structure of the branched-chain keto acid decarboxylase (kdca) from lactococcus lactis with 2R-1- hydroxyethyl-deazathdp
Analyse The complex structure 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
- 2VBG
- Type
- protein
- Length
- 1,090 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Branched-chain alpha-ketoacid decarboxylase
- UniProt
- Q6QBS4
- Ligands
- R1T, MG
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Branched-chain alpha-ketoacid decarboxylase | protein | 546 | 42% helix, 18% strand | Q6QBS4 |
| B | Branched-chain alpha-ketoacid decarboxylase | protein | 544 | 42% helix, 18% strand | Q6QBS4 |
Ligands and binding sites
- R1T · 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-[(1R)-1-hydroxyethyl]-3-methyl-2-thienyl}ethyl trihydrogen 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
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.82 | 0.97 | 41 | MG, R1T |
| 2 | 192 | 0.82 | 0.96 | 38 | MG, R1T |
| 3 | 364 | 0.61 | 0.78 | 34 | empty |
| 4 | 228 | 0.56 | 0.78 | 28 | empty |
| 5 | 70 | 0.45 | 0.83 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 3491 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 2VBG · The complex structure of the branched-chain keto acid decarboxylase (KdcA) from… · 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 2VBG · PDBe 2VBG · UniProt Q6QBS4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.