Research workbench
Crystal structure of xylose isomerase from piromyces E2 complexed with one MG2+ ion and xylitol
Analyse Crystal structure of xylose isomerase from piromyces E2 complexed with one MG2+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NH6
- Type
- protein
- Length
- 1,743 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- Q9P8C9
- Ligands
- XYL, MG, SO4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Xylose isomerase (EC 5.3.1.5) | protein | 436 | 49% helix, 12% strand | Q9P8C9 |
| D | Xylose isomerase (EC 5.3.1.5) | protein | 435 | 49% helix, 12% strand | Q9P8C9 |
Ligands and binding sites
- XYL · Xylitol · ligand · 4 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.90 | 0.92 | 176 | XYL |
| 2 | 444 | 0.86 | 0.93 | 60 | empty |
| 3 | 938 | 0.85 | 0.87 | 82 | empty |
| 4 | 1173 | 0.85 | 0.86 | 145 | XYL |
| 5 | 334 | 0.73 | 0.85 | 52 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4301 Ų buried · 54 hydrogen bonds · protein-protein
- B–D · 4287 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 1950 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1945 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1490 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5NH6 · Crystal structure of xylose isomerase from Piromyces E2 Complexed with one Mg2+ ion 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 Q9P8C9
- Elsewhere: RCSB PDB 5NH6 · PDBe 5NH6 · UniProt Q9P8C9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.