MolNFT v1 · #166742 · protein
Crystal structure of dihydrolipoyl dehydrogenase from elizabethkingia anophelis NUHP1
6UZI: “Crystal structure of dihydrolipoyl dehydrogenase from elizabethkingia anophelis NUHP1”. X-ray diffraction, 3 ligands (FAD, ZN, CL), 12 pockets (best druggability 0.83). MolNFT v1 #166742 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6UZI
- Type
- protein
- Length
- 1,870 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase
- EC
- 1.8.1.4
- UniProt
- A0A077ELH4
- Ligands
- FAD, ZN, CL
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 467 | 34% helix, 27% strand | A0A077ELH4 |
| C | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 470 | 34% helix, 27% strand | A0A077ELH4 |
| D | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 466 | 35% helix, 27% strand | A0A077ELH4 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.83 | 0.84 | 111 | FAD, EDO |
| 2 | 651 | 0.83 | 0.87 | 58 | EDO |
| 3 | 586 | 0.82 | 0.87 | 58 | empty |
| 4 | 1150 | 0.80 | 0.81 | 110 | FAD, EDO |
| 5 | 838 | 0.80 | 0.83 | 98 | FAD |
Interfaces
3 interfaces between chains.
- C–D · 3882 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 3875 Ų buried · 58 hydrogen bonds · protein-protein
- A–C · 701 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6UZI · Crystal structure of Dihydrolipoyl dehydrogenase from Elizabethkingia anophelis NUHP1 · 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 A0A077ELH4
- Elsewhere: RCSB PDB 6UZI · PDBe 6UZI · UniProt A0A077ELH4
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