MolNFT v1 · #54212 · protein
Probing the active site of the sugar isomerase domain from E. COLI arabinose-5-phosphate isomerase via X-ray crystallography
2XHZ · Arabinose 5-phosphate isomerase: “Probing the active site of the sugar isomerase domain from E. COLI arabinose-5-phosphate isomerase via X-ray…”. X-ray diffraction, 3 pockets (best druggability 0.85). MolNFT v1 #54212 on GenesisL1…
- PDB
- 2XHZ
- Type
- protein
- Length
- 693 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arabinose 5-phosphate isomerase
- EC
- 5.3.1.13
- UniProt
- P45395
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Arabinose 5-phosphate isomerase (EC 5.3.1.13) | protein | 173 | 50% helix, 13% strand | P45395 |
| B | Arabinose 5-phosphate isomerase (EC 5.3.1.13) | protein | 174 | 52% helix, 13% strand | P45395 |
| D | Arabinose 5-phosphate isomerase (EC 5.3.1.13) | protein | 173 | 53% helix, 13% strand | P45395 |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.85 | 0.87 | 119 | empty |
| 2 | 156 | 0.57 | 0.82 | 39 | empty |
| 3 | 159 | 0.51 | 0.79 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2193 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2166 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 627 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 564 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 286 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2XHZ · Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- P45395 · AlphaFold monomer V2.0 prediction for arabinose 5-phosphate isomerase kdsd (P45395) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P45395
- Elsewhere: RCSB PDB 2XHZ · PDBe 2XHZ · UniProt P45395
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