MolNFT v1 · #104549 · protein
Room temperature X-ray structure of D-xylose isomerase in complex with two NI2+ ions and L-ribulose
4QE4: “Room temperature X-ray structure of D-xylose isomerase in complex with two NI2+ ions and L-ribulose”. X-ray diffraction, 2 ligands (34V, NI), 4 pockets (best druggability 0.71). MolNFT v1 #104549 on GenesisL1: 3D structure, binding…
- PDB
- 4QE4
- Type
- protein
- Length
- 388 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P24300
- Ligands
- 34V, NI
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylose isomerase (EC 5.3.1.5) | protein | 388 | 50% helix, 10% strand | P24300 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.71 | 0.98 | 22 | empty |
| 2 | 479 | 0.65 | 0.77 | 46 | NI, 34V |
| 3 | 84 | 0.48 | 0.82 | 14 | empty |
| 4 | 60 | 0.35 | 0.78 | 14 | empty |
Compared structures
- 4QE4 · Room temperature X-ray structure of D-xylose isomerase in complex with two Ni2+ 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 P24300
- Elsewhere: RCSB PDB 4QE4 · PDBe 4QE4 · UniProt P24300
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