MolNFT v1 · #93931 · protein
Crystal structure of a mutant, G219A, of glucose isomerase from streptomyces sp. sk
4HHM · Xylose isomerase: “Crystal structure of a mutant, G219A, of glucose isomerase from streptomyces sp. sk”. X-ray diffraction, 2 ligands (CO, MG), 20 pockets (best druggability 0.87). MolNFT v1 #93931 on GenesisL1: 3D structure…
- PDB
- 4HHM
- Type
- protein
- Length
- 3,088 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- Q9ZAI3
- Ligands
- CO, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Xylose isomerase (EC 5.3.1.5) | protein | 386 | 49% helix, 10% strand | Q9ZAI3 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
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 | 717 | 0.87 | 0.91 | 109 | empty |
| 2 | 573 | 0.87 | 0.92 | 87 | empty |
| 3 | 635 | 0.86 | 0.90 | 96 | empty |
| 4 | 646 | 0.86 | 0.90 | 101 | empty |
| 5 | 817 | 0.79 | 0.82 | 94 | CO |
Interfaces
16 interfaces between chains.
- C–D · 4858 Ų buried · 69 hydrogen bonds · protein-protein
- G–H · 4845 Ų buried · 74 hydrogen bonds · protein-protein
- A–B · 4820 Ų buried · 73 hydrogen bonds · protein-protein
- E–F · 4798 Ų buried · 72 hydrogen bonds · protein-protein
- F–G · 1583 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4HHM · Crystal structure of a mutant, G219A, 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 4HHM · PDBe 4HHM · UniProt Q9ZAI3
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