MolNFT v1 · #68962 · protein
Room temperature X-ray structure of D-xylose isomerase complexed with 2CD(2+) co-factors and D12-D-alpha-glucose in the cyclic form
3KBM: “Room temperature X-ray structure of D-xylose isomerase complexed with 2CD(2+) co-factors and…”. X-ray diffraction, 2 ligands (GLC, CD), 3 pockets (best druggability 0.72). MolNFT v1 #68962 on GenesisL1: 3D structure, binding sites…
- PDB
- 3KBM
- 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
- GLC, CD
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylose isomerase (EC 5.3.1.5) | protein | 388 | 50% 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 | 22 | empty |
| 2 | 490 | 0.66 | 0.78 | 46 | GLC |
| 3 | 79 | 0.42 | 0.79 | 13 | empty |
Compared structures
- 3KBM · Room Temperature X-ray structure of D-Xylose Isomerase complexed with 2Cd(2+) co-factors… · the same entry in another collection · chain A against A, TM-score 1.00
- P24300 · AlphaFold monomer V2.0 prediction for xylose isomerase (P24300) · a predicted model of the same protein · 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 3KBM · PDBe 3KBM · UniProt P24300
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