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Crystal structure of a cubic core of the dihydrolipoamide acyltransferase (E2B) component in the branched-chain alpha-ketoacid dehydrogenase complex (bckdc), coenzyme a-bound form
Analyse Crystal structure of a cubic core of the dihydrolipoamide acyltransferase (E2B)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2II4
- Type
- protein
- Length
- 1,872 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase…
- EC
- 2.3.1.168
- UniProt
- P11181
- Ligands
- COA, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.168) | protein | 234 | 38% helix, 26% strand | P11181 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.79 | 0.98 | 32 | empty |
| 2 | 105 | 0.78 | 0.98 | 32 | empty |
| 3 | 151 | 0.78 | 0.95 | 30 | CL |
| 4 | 130 | 0.77 | 0.95 | 27 | CL |
| 5 | 177 | 0.76 | 0.92 | 23 | CL |
Interfaces
7 interfaces between chains.
- E–F · 1507 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1495 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1492 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1484 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1482 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2II4 · Crystal structure of a cubic core of the dihydrolipoamide acyltransferase (E2b) component… · the same entry in another collection · chain G against G, TM-score 1.00
- P11181 · AlphaFold monomer V2.0 prediction for lipoamide acyltransferase component of… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P11181
- Elsewhere: RCSB PDB 2II4 · PDBe 2II4 · UniProt P11181
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