MolNFT v1 · #104535 · protein
Joint X-ray and neutron structure of streptomyces rubiginosus D-xylose isomerase in complex with two CD2+ ions and cyclic beta-L-arabinose
4QDP: “Joint X-ray and neutron structure of streptomyces rubiginosus D-xylose isomerase in complex with two CD2+…”. Neutron diffraction; x-ray diffraction, 2 ligands (ARB, CD), 3 pockets (best druggability 0.72). MolNFT v1 #104535 on…
- PDB
- 4QDP
- Type
- protein
- Length
- 388 residues
- Chains
- 1
- Method
- neutron diffraction; x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P24300
- Ligands
- ARB, CD
- Pockets
- 3 · best druggability 0.72
Structure
neutron diffraction; x-ray diffraction · 1 distinct chain · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylose isomerase (EC 5.3.1.5) | protein | 388 | 49% helix, 11% strand | P24300 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.72 | 0.98 | 24 | empty |
| 2 | 485 | 0.66 | 0.78 | 47 | ARB |
| 3 | 69 | 0.41 | 0.80 | 13 | empty |
Compared structures
- 4QDP · Joint X-ray and neutron structure of Streptomyces rubiginosus D-xylose isomerase in… · 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 4QDP · PDBe 4QDP · UniProt P24300
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