Research workbench
Crystal structure of xylose isomerase from piromyces sp. E2
Analyse Crystal structure of xylose isomerase from piromyces sp. E2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YN3
- Type
- protein
- Length
- 1,740 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
- MN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Xylose isomerase (EC 5.3.1.5) | protein | 435 | 48% helix, 12% strand | Q9P8C9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.86 | 0.89 | 83 | empty |
| 2 | 408 | 0.85 | 0.93 | 59 | empty |
| 3 | 170 | 0.80 | 0.96 | 37 | empty |
| 4 | 171 | 0.80 | 0.95 | 34 | empty |
| 5 | 410 | 0.77 | 0.86 | 50 | empty |
Interfaces
6 interfaces between chains.
- A–D · 4344 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 4341 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 2022 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1975 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1481 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5YN3 · Crystal structure of xylose isomerase from Piromyces sp. E2 · 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 5YN3 · PDBe 5YN3 · UniProt Q9P8C9
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