MolNFT v1 · #78418 · protein
Structure of dihydrodipicolinate synthase complexed with 3- hydroxypropanoic ACID(HPA)AT 2.70 a resolution
3S8H: “Structure of dihydrodipicolinate synthase complexed with 3- hydroxypropanoic ACID(HPA)AT 2.70 a resolution”. X-ray diffraction, 1 ligand (3OH), 3 pockets (best druggability 0.74). MolNFT v1 #78418 on GenesisL1: 3D structure, binding…
- PDB
- 3S8H
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- Q9I4W3
- Ligands
- 3OH
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 292 | 48% helix, 13% strand | Q9I4W3 |
Ligands and binding sites
- 3OH · 3-hydroxy-propanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.74 | 0.84 | 58 | 3OH |
| 2 | 134 | 0.52 | 0.81 | 30 | 3OH |
| 3 | 137 | 0.48 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1569 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3S8H · Structure of dihydrodipicolinate synthase complexed with 3-Hydroxypropanoic acid(HPA)at… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I4W3 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q9I4W3) · a predicted model of the same protein · chain B 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 Q9I4W3
- Elsewhere: RCSB PDB 3S8H · PDBe 3S8H · UniProt Q9I4W3
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