MolNFT v1 · #59182 · protein
Hexagonal kristal form of 2-keto-3-deoxyarabinonate dehydratase
3BQB · Putative uncharacterized protein: “Hexagonal kristal form of 2-keto-3-deoxyarabinonate dehydratase”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.67). MolNFT v1 #59182 on GenesisL1: 3D structure, binding sites…
- PDB
- 3BQB
- Type
- protein
- Length
- 1,137 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q97UA0
- Ligands
- MG
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, Z, Y | Putative uncharacterized protein | protein | 282 | 20% helix, 38% strand | Q97UA0 |
| X | Putative uncharacterized protein | protein | 291 | 20% helix, 39% strand | Q97UA0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, X, Z, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.67 | 0.80 | 46 | MG |
| 2 | 194 | 0.56 | 0.80 | 28 | MG |
| 3 | 177 | 0.56 | 0.80 | 25 | MG |
| 4 | 146 | 0.53 | 0.80 | 20 | MG |
| 5 | 114 | 0.37 | 0.74 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–X · 1944 Ų buried · 33 hydrogen bonds · protein-protein
- Z–Y · 1921 Ų buried · 36 hydrogen bonds · protein-protein
- A–Z · 705 Ų buried · 21 hydrogen bonds · protein-protein
- X–Y · 688 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3BQB · Hexagonal kristal form of 2-keto-3-deoxyarabinonate dehydratase · the same entry in another collection · chain A against A, TM-score 1.00
- Q97UA0 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxy-D-arabinonate dehydratase (Q97UA0) · a predicted model of the same protein · chain A 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 Q97UA0
- Elsewhere: RCSB PDB 3BQB · PDBe 3BQB · UniProt Q97UA0
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