MolNFT v1 · #5241 · protein
Homoserine dehydrogenase complex with NAD analogue and L- homoserine
1EBU: “Homoserine dehydrogenase complex with NAD analogue and L- homoserine”. X-ray diffraction, 3 ligands (NDA, HSE, NA), 17 pockets (best druggability 0.80). MolNFT v1 #5241 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1EBU
- Type
- protein
- Length
- 1,432 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoserine dehydrogenase
- EC
- 1.1.1.3
- UniProt
- P31116
- Ligands
- NDA, HSE, NA
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 358 | 39% helix, 20% strand | P31116 |
Ligands and binding sites
- NDA · 3-aminomethyl-pyridinium-adenine-dinucleotide · ligand · chains D
- HSE · L-homoserine · ligand · chains D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.80 | 0.81 | 93 | empty |
| 2 | 1165 | 0.79 | 0.80 | 104 | empty |
| 3 | 419 | 0.64 | 0.78 | 46 | empty |
| 4 | 367 | 0.62 | 0.78 | 39 | NDA, HSE |
| 5 | 369 | 0.60 | 0.77 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1767 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1741 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1EBU · Homoserine dehydrogenase complex with NAD analogue and L-homoserine · the same entry in another collection · chain D against D, TM-score 1.00
- P31116 · AlphaFold monomer V2.0 prediction for homoserine dehydrogenase (P31116) · 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 P31116
- Elsewhere: RCSB PDB 1EBU · PDBe 1EBU · UniProt P31116
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