MolNFT v1 · #66232 · protein
Crystal structure of uronate isomerase from bacillus halodurans complexed with zinc and D-fructuronate
3HKA: “Crystal structure of uronate isomerase from bacillus halodurans complexed with zinc and D-fructuronate”. X-ray diffraction, 4 ligands (FIX, ZN, CO3), 10 pockets (best druggability 0.65). MolNFT v1 #66232 on GenesisL1: 3D structure…
- PDB
- 3HKA
- Type
- protein
- Length
- 1,233 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uronate isomerase
- UniProt
- Q9KFI6
- Ligands
- FIX, ZN, CO3, CL
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Uronate isomerase | protein | 411 | 56% helix, 9% strand | Q9KFI6 |
Ligands and binding sites
- FIX · D-fructuronic acid · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 4 copies · chains A, B, C
- CO3 · Carbonate ion · ion · 3 copies · chains A, C, B
- CL · Chloride ion · ion · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 675 | 0.65 | 0.75 | 75 | ZN |
| 2 | 363 | 0.63 | 0.78 | 42 | FIX |
| 3 | 363 | 0.62 | 0.78 | 42 | FIX |
| 4 | 392 | 0.62 | 0.77 | 43 | FIX, ZN |
| 5 | 214 | 0.51 | 0.76 | 31 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2059 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2047 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2006 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 3HKA · Crystal structure of uronate isomerase from Bacillus halodurans complexed with zinc and… · the same entry in another collection · chain A 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 Q9KFI6
- Elsewhere: RCSB PDB 3HKA · PDBe 3HKA · UniProt Q9KFI6
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