MolNFT v1 · #70117 · protein
Crystal structure of the 3-dehydroquinate dehydratase (arod) from salmonella typhimurium LT2 with citrate bound to the active site.
3LB0: “Crystal structure of the 3-dehydroquinate dehydratase (arod) from salmonella typhimurium LT2 with citrate…”. X-ray diffraction, 7 pockets (best druggability 0.65). MolNFT v1 #70117 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3LB0
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- P58687
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 259 | 42% helix, 20% strand | P58687 |
| B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 251 | 45% helix, 22% strand | P58687 |
Ligands and binding sites
- CIT · Citric acid · additive · chains A
- FMT · Formic acid · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.65 | 0.94 | 16 | CIT |
| 2 | 195 | 0.52 | 0.77 | 25 | TRS |
| 3 | 81 | 0.46 | 0.82 | 23 | empty |
| 4 | 91 | 0.44 | 0.80 | 21 | empty |
| 5 | 82 | 0.43 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1006 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3LB0 · Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium… · the same entry in another collection · chain B against B, TM-score 1.00
- P58687 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (P58687) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P58687
- Elsewhere: RCSB PDB 3LB0 · PDBe 3LB0 · UniProt P58687
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