Research workbench
Protein engineering of xylose (glucose) isomerase from actinoplanes missouriensis. 1. crystallography and site-directed mutagenesis of metal binding sites
Analyse Protein engineering of xylose (glucose) isomerase from actinoplanes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XIM
- Type
- protein
- Length
- 1,568 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P12851
- Ligands
- XLS, MG
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-xylose isomerase (EC 5.3.1.5) | protein | 392 | 50% helix, 10% strand | P12851 |
Ligands and binding sites
- XLS · D-xylose · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.84 | 0.86 | 101 | empty |
| 2 | 804 | 0.83 | 0.86 | 105 | empty |
| 3 | 551 | 0.79 | 0.86 | 61 | XLS |
| 4 | 569 | 0.79 | 0.85 | 58 | XLS |
| 5 | 591 | 0.79 | 0.84 | 64 | XLS, MG |
Interfaces
6 interfaces between chains.
- A–C · 5009 Ų buried · 84 hydrogen bonds · protein-protein
- B–D · 5001 Ų buried · 83 hydrogen bonds · protein-protein
- A–B · 1739 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1732 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1686 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6XIM · Protein engineering of xylose (glucose) isomerase from actinoplanes missouriensis. 1.… · the same entry in another collection · chain A against A, TM-score 1.00
- P12851 · AlphaFold monomer V2.0 prediction for xylose isomerase (P12851) · a predicted model of the same protein · 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 P12851
- Elsewhere: RCSB PDB 6XIM · PDBe 6XIM · UniProt P12851
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