Research workbench
Crystal structure of native xylose isomerase from piromyces E2
Analyse Crystal structure of native xylose isomerase from piromyces E2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NH5
- 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
- CA, FE2, MG, 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
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C, D
- GOL · Glycerol · additive · 20 copies · chains A, B, D, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.87 | 0.94 | 58 | empty |
| 2 | 447 | 0.86 | 0.93 | 61 | empty |
| 3 | 959 | 0.86 | 0.87 | 85 | empty |
| 4 | 1146 | 0.85 | 0.86 | 141 | GOL |
| 5 | 1140 | 0.85 | 0.86 | 140 | GOL |
Interfaces
6 interfaces between chains.
- C–D · 4279 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 4253 Ų buried · 53 hydrogen bonds · protein-protein
- A–D · 1944 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1933 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 1492 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5NH5 · Crystal structure of native xylose isomerase from Piromyces 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 5NH5 · PDBe 5NH5 · UniProt Q9P8C9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.