Research workbench
Crystal structure of apo xylose isomerase from piromyces E2
Analyse Crystal structure of apo 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
- 5NHM
- Type
- protein
- Length
- 1,742 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
- SO4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Xylose isomerase (EC 5.3.1.5) | protein | 436 | 49% helix, 12% strand | Q9P8C9 |
| B, C | Xylose isomerase (EC 5.3.1.5) | protein | 435 | 49% helix, 12% strand | Q9P8C9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 2 copies · chains A, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.90 | 0.92 | 175 | GOL |
| 2 | 437 | 0.86 | 0.94 | 57 | empty |
| 3 | 921 | 0.86 | 0.87 | 84 | empty |
| 4 | 1148 | 0.85 | 0.86 | 147 | GOL |
| 5 | 298 | 0.75 | 0.87 | 53 | ACY |
Interfaces
6 interfaces between chains.
- A–B · 4294 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 4277 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 1981 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1979 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1498 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5NHM · Crystal structure of apo 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 5NHM · PDBe 5NHM · UniProt Q9P8C9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.