MolNFT v1 · #93930 · protein
High resolution crystal structure of glucose isomerase from streptomyces sp. sk
4HHL · Xylose isomerase: “High resolution crystal structure of glucose isomerase from streptomyces sp. sk”. X-ray diffraction, 2 ligands (MG, CO), 7 pockets (best druggability 0.74). MolNFT v1 #93930 on GenesisL1: 3D structure, binding…
- PDB
- 4HHL
- Type
- protein
- Length
- 771 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- Q9ZAI3
- Ligands
- MG, CO
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylose isomerase (EC 5.3.1.5) | protein | 386 | 49% helix, 10% strand | Q9ZAI3 |
| B | Xylose isomerase (EC 5.3.1.5) | protein | 385 | 50% helix, 11% strand | Q9ZAI3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.74 | 0.99 | 23 | empty |
| 2 | 518 | 0.66 | 0.77 | 52 | empty |
| 3 | 480 | 0.65 | 0.77 | 44 | empty |
| 4 | 253 | 0.60 | 0.80 | 39 | EDO |
| 5 | 230 | 0.59 | 0.80 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 4901 Ų buried · 77 hydrogen bonds · protein-protein
Compared structures
- 4HHL · High resolution crystal structure of Glucose Isomerase from Streptomyces sp. SK · 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 Q9ZAI3
- Elsewhere: RCSB PDB 4HHL · PDBe 4HHL · UniProt Q9ZAI3
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