Research workbench
Crystal structure of uronate isomerase from bacillus halodurans complexed with zinc and D-arabinarate, monoclinic crystal form
Analyse Crystal structure of uronate isomerase from bacillus halodurans complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HK7
- Type
- protein
- Length
- 4,956 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uronate isomerase
- UniProt
- Q9KFI6
- Ligands
- RAT, ZN, NA, CO3, CL
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Uronate isomerase | protein | 413 | 57% helix, 9% strand | Q9KFI6 |
Ligands and binding sites
- RAT · D-arabinaric acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CO3 · Carbonate ion · ion · 12 copies · chains A, B, C, D, F, E, G, I, H, J, L, K
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.73 | 0.77 | 91 | NA |
| 2 | 855 | 0.72 | 0.77 | 101 | NA |
| 3 | 528 | 0.70 | 0.79 | 45 | empty |
| 4 | 537 | 0.70 | 0.79 | 44 | empty |
| 5 | 391 | 0.69 | 0.82 | 41 | empty |
Interfaces
28 interfaces between chains.
- A–C · 2061 Ų buried · 37 hydrogen bonds · protein-protein
- K–L · 2055 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 2054 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 2049 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 2047 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3HK7 · Crystal structure of uronate isomerase from Bacillus halodurans complexed with zinc and… · the same entry in another collection · chain I against I, 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 3HK7 · PDBe 3HK7 · UniProt Q9KFI6
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