MolNFT v1 · #110043 · protein
Crystal structure of xylose isomerase from an human intestinal tract microbe bacteroides thetaiotaomicron
4XKM: “Crystal structure of xylose isomerase from an human intestinal tract microbe bacteroides thetaiotaomicron”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.90). MolNFT v1 #110043 on GenesisL1: 3D structure, binding…
- PDB
- 4XKM
- Type
- protein
- Length
- 3,480 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- Q8A9M2
- Ligands
- MN
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Xylose isomerase (EC 5.3.1.5) | protein | 435 | 46% helix, 12% strand | Q8A9M2 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.90 | 0.95 | 113 | empty |
| 2 | 1125 | 0.90 | 0.92 | 149 | MN |
| 3 | 1151 | 0.89 | 0.90 | 123 | empty |
| 4 | 361 | 0.86 | 0.95 | 60 | empty |
| 5 | 922 | 0.85 | 0.87 | 77 | empty |
Interfaces
13 interfaces between chains.
- D–E · 4213 Ų buried · 50 hydrogen bonds · protein-protein
- B–H · 4195 Ų buried · 52 hydrogen bonds · protein-protein
- A–G · 4160 Ų buried · 49 hydrogen bonds · protein-protein
- C–F · 4151 Ų buried · 49 hydrogen bonds · protein-protein
- C–E · 2073 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 4XKM · Crystal structure of Xylose Isomerase from an human intestinal tract microbe Bacteroides… · the same entry in another collection · chain H against H, TM-score 1.00
- Q8A9M2 · AlphaFold monomer V2.0 prediction for xylose isomerase (Q8A9M2) · 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 Q8A9M2
- Elsewhere: RCSB PDB 4XKM · PDBe 4XKM · UniProt Q8A9M2
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