MolNFT v1 · #35943 · protein
Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdp
2EQ8 · Pyruvate dehydrogenase complex, dihydrolipoamide…: “Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdp”. X-ray diffraction, 1 ligand (FAD), 16 pockets (best druggability 0.82). MolNFT v1 #35943 on…
- PDB
- 2EQ8
- Type
- protein
- Length
- 1,918 residues
- Chains
- 6
- 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, 2.3.1.12
- UniProt
- Q5SLR0, Q5SLV9
- Ligands
- FAD
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component (EC 1.8.1.4) | protein | 460 | 35% helix, 27% strand | Q5SLR0 |
| C, F | Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component (EC 2.3.1.12) | protein | 39 | 54% helix, 0% strand | Q5SLV9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.82 | 0.85 | 67 | empty |
| 2 | 814 | 0.82 | 0.85 | 70 | empty |
| 3 | 877 | 0.80 | 0.82 | 97 | FAD |
| 4 | 899 | 0.79 | 0.82 | 98 | FAD |
| 5 | 898 | 0.79 | 0.82 | 96 | FAD |
Interfaces
7 interfaces between chains.
- D–E · 3897 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 3878 Ų buried · 43 hydrogen bonds · protein-protein
- D–F · 481 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 476 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 244 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2EQ8 · Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdp · the same entry in another collection · chain E against E, 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 Q5SLV9
- Elsewhere: RCSB PDB 2EQ8 · PDBe 2EQ8 · UniProt Q5SLR0 · UniProt Q5SLV9
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