Research workbench
Xylose isomerase from paenibacillus sp. R4
Analyse Xylose isomerase from paenibacillus sp. R4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6INT
- Type
- protein
- Length
- 3,302 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- Ligands
- CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F, G, H | Xylose isomerase | protein | 413 | 50% helix, 12% strand | — |
| B, E | Xylose isomerase | protein | 412 | 51% helix, 12% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 24 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 | 873 | 0.87 | 0.89 | 85 | empty |
| 2 | 877 | 0.87 | 0.89 | 84 | empty |
| 3 | 849 | 0.87 | 0.89 | 77 | empty |
| 4 | 940 | 0.87 | 0.88 | 95 | empty |
| 5 | 618 | 0.86 | 0.91 | 56 | empty |
Interfaces
16 interfaces between chains.
- A–B · 4248 Ų buried · 55 hydrogen bonds · protein-protein
- G–H · 4231 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 4224 Ų buried · 62 hydrogen bonds · protein-protein
- E–F · 4220 Ų buried · 60 hydrogen bonds · protein-protein
- F–G · 2083 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 6INT · xylose isomerase from Paenibacillus sp. R4 · 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
- Elsewhere: RCSB PDB 6INT · PDBe 6INT
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