Research workbench
Cryo-EM structure of the dihydrolipoyl transacetylase cubic core of the E. COLI pyruvate dehydrogenase complex including lipoyl domains
Analyse Cryo-EM structure of the dihydrolipoyl transacetylase cubic core of the E. COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B9K
- Type
- protein
- Length
- 7,680 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
- EC
- 2.3.1.12
- UniProt
- P06959
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 1 distinct chain · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12) | protein | 320 | 27% helix, 26% strand | P06959 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.81 | 0.87 | 55 | empty |
| 2 | 534 | 0.81 | 0.87 | 63 | empty |
| 3 | 528 | 0.80 | 0.87 | 64 | empty |
| 4 | 542 | 0.80 | 0.87 | 60 | empty |
| 5 | 527 | 0.80 | 0.87 | 63 | empty |
Interfaces
36 interfaces between chains.
- D–E · 2321 Ų buried · 24 hydrogen bonds · protein-protein
- N–O · 2298 Ų buried · 22 hydrogen bonds · protein-protein
- S–U · 2295 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 2294 Ų buried · 22 hydrogen bonds · protein-protein
- T–U · 2293 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (nonstandard).
Compared structures
- 7B9K · Cryo-EM structure of the dihydrolipoyl transacetylase cubic core of the E. coli pyruvate… · 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 P06959
- Elsewhere: RCSB PDB 7B9K · PDBe 7B9K · UniProt P06959
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