Research workbench
Crystal structure of a cubic core of the dihydrolipoamide acyltransferase (E2B) component in the branched-chain alpha-ketoacid dehydrogenase complex (bckdc), isobutyryl-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
- 2II5
- 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
- CO6, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 39% 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 | 39% helix, 26% strand | P11181 |
Ligands and binding sites
- CO6 · Isobutyryl-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
- ACT · Acetate ion · additive · 16 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.83 | 0.94 | 54 | CL |
| 2 | 178 | 0.78 | 0.94 | 35 | CL |
| 3 | 100 | 0.77 | 0.97 | 30 | empty |
| 4 | 180 | 0.77 | 0.93 | 32 | CL |
| 5 | 156 | 0.76 | 0.93 | 24 | CL |
Interfaces
7 interfaces between chains.
- D–F · 1487 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1483 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1476 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1474 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1468 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2II5 · Crystal structure of a cubic core of the dihydrolipoamide acyltransferase (E2b) component… · the same entry in another collection · chain H against H, 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 2II5 · PDBe 2II5 · UniProt P11181
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