Research workbench
Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdb
Analyse Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EQ9
- Type
- protein
- Length
- 3,840 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component; Pyruvate…
- EC
- 1.8.1.4, 2.3.1.168
- UniProt
- Q5SLR0, Q5SLR1
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, G, H, J, K | Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component (EC 1.8.1.4) | protein | 460 | 35% helix, 28% strand | Q5SLR0 |
| C, F, I, L | Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component (EC 2.3.1.168) | protein | 40 | 50% helix, 5% strand | Q5SLR1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, D, E, G, H, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1042 | 0.85 | 0.86 | 120 | FAD |
| 2 | 1005 | 0.84 | 0.85 | 115 | FAD |
| 3 | 763 | 0.83 | 0.86 | 69 | empty |
| 4 | 767 | 0.83 | 0.86 | 62 | empty |
| 5 | 839 | 0.83 | 0.85 | 64 | empty |
Interfaces
16 interfaces between chains.
- G–H · 3882 Ų buried · 45 hydrogen bonds · protein-protein
- J–K · 3851 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 3844 Ų buried · 44 hydrogen bonds · protein-protein
- D–E · 3832 Ų buried · 46 hydrogen bonds · protein-protein
- B–K · 721 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2EQ9 · Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdb · 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 Q5SLR0
- Every structure of UniProt Q5SLR1
- Elsewhere: RCSB PDB 2EQ9 · PDBe 2EQ9 · UniProt Q5SLR0 · UniProt Q5SLR1
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