Research workbench
Crystal structure of human dihydrolipoamide dehydrogenase (E3) complexed to the E3-binding domain of human E3-binding protein
Analyse Crystal structure of human dihydrolipoamide dehydrogenase (E3) complexed to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F5Z
- Type
- protein
- Length
- 4,930 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase; Pyruvate dehydrogenase protein X component
- EC
- 1.8.1.4
- UniProt
- P09622, O00330
- Ligands
- FAD, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, H, J | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 472 | 35% helix, 27% strand | P09622 |
| B, D, F | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 471 | 34% helix, 27% strand | P09622 |
| I | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 470 | 36% helix, 26% strand | P09622 |
| K, L, M, N, O | Pyruvate dehydrogenase protein X component | protein | 43 | 58% helix, 5% strand | O00330 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- SO4 · Sulfate ion · ion · 39 copies · chains A, B, C, E, D, F, G, H, I, J
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 | 778 | 0.84 | 0.87 | 72 | SO4 |
| 2 | 791 | 0.84 | 0.87 | 77 | empty |
| 3 | 831 | 0.84 | 0.86 | 71 | SO4 |
| 4 | 826 | 0.84 | 0.86 | 74 | SO4 |
| 5 | 780 | 0.83 | 0.86 | 66 | SO4 |
Interfaces
22 interfaces between chains.
- I–J · 4028 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 3997 Ų buried · 61 hydrogen bonds · protein-protein
- E–F · 3985 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3970 Ų buried · 59 hydrogen bonds · protein-protein
- G–H · 3966 Ų buried · 62 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2F5Z · Crystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Complexed to the… · the same entry in another collection · chain J against J, 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 P09622
- Every structure of UniProt O00330
- Elsewhere: RCSB PDB 2F5Z · PDBe 2F5Z · UniProt P09622 · UniProt O00330
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.