MolNFT v1 · #4754 · protein
Dihydrolipoamide dehydrogenase of glycine decarboxylase from pisum sativum
1DXL: “Dihydrolipoamide dehydrogenase of glycine decarboxylase from pisum sativum”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.84). MolNFT v1 #4754 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1DXL
- Type
- protein
- Length
- 1,868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoamide dehydrogenase
- EC
- 1.8.1.4
- UniProt
- P31023
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydrolipoamide dehydrogenase (EC 1.8.1.4) | protein | 467 | 33% helix, 25% strand | P31023 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.84 | 0.87 | 59 | empty |
| 2 | 742 | 0.83 | 0.87 | 61 | empty |
| 3 | 811 | 0.82 | 0.84 | 103 | FAD |
| 4 | 573 | 0.81 | 0.87 | 73 | empty |
| 5 | 836 | 0.80 | 0.83 | 94 | FAD |
Interfaces
5 interfaces between chains.
- C–D · 3902 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 3871 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 256 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 253 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 120 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1DXL · Dihydrolipoamide dehydrogenase of glycine decarboxylase from Pisum Sativum · the same entry in another collection · chain D against D, TM-score 1.00
- P31023 · AlphaFold monomer V2.0 prediction for dihydrolipoyl dehydrogenase, mitochondrial (P31023) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P31023
- Elsewhere: RCSB PDB 1DXL · PDBe 1DXL · UniProt P31023
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