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1.85 ångström crystal structure of the 3-dehydroquinate dehydratase (arod) from salmonella typhimurium LT2.
Analyse 1.85 ångström crystal structure of the 3-dehydroquinate dehydratase (arod) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L2I
- Type
- protein
- Length
- 509 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
- Ligands
- MG
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 256 | 44% helix, 21% strand | P58687 |
| B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 253 | 45% helix, 21% strand | P58687 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.61 | 0.80 | 33 | empty |
| 2 | 162 | 0.50 | 0.78 | 21 | empty |
| 3 | 87 | 0.45 | 0.81 | 20 | MG |
| 4 | 51 | 0.43 | 0.83 | 15 | empty |
| 5 | 62 | 0.41 | 0.81 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1069 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3L2I · 1.85 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from… · the same entry in another collection · chain A against A, TM-score 1.00
- P58687 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (P58687) · a predicted model of the same protein · chain B 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 3L2I · PDBe 3L2I · UniProt P58687
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