MolNFT v1 · #128130 · protein
Crystal structure of xylose isomerase from piromyces E2 in complex with two CD2+ ions and xylose
5NHE: “Crystal structure of xylose isomerase from piromyces E2 in complex with two CD2+ ions and xylose”. X-ray diffraction, 5 ligands (XLS, XYP, XYS), 20 pockets (best druggability 0.87). MolNFT v1 #128130 on GenesisL1: 3D structure…
- PDB
- 5NHE
- Type
- protein
- Length
- 1,744 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
- XLS, XYP, XYS, CD, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Xylose isomerase (EC 5.3.1.5) | protein | 436 | 49% helix, 12% strand | Q9P8C9 |
Ligands and binding sites
- XLS · D-xylose · ligand · 2 copies · chains A, C, B, D
- XYP · beta-D-xylopyranose · sugar · 8 copies · chains A, C, D, B
- XYS · alpha-D-xylopyranose · sugar · 6 copies · chains A, B, C, D
- CD · Cadmium ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, 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 | 730 | 0.87 | 0.90 | 106 | XLS, XYS |
| 2 | 411 | 0.86 | 0.94 | 58 | empty |
| 3 | 428 | 0.86 | 0.94 | 60 | empty |
| 4 | 942 | 0.86 | 0.87 | 82 | empty |
| 5 | 1128 | 0.84 | 0.85 | 110 | XLS, XYS |
Interfaces
6 interfaces between chains.
- C–D · 4337 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 4317 Ų buried · 56 hydrogen bonds · protein-protein
- A–D · 1963 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1959 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1490 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 5NHE · Crystal structure of xylose isomerase from Piromyces E2 in complex with two Cd2+ ions 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 5NHE · PDBe 5NHE · UniProt Q9P8C9
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