Research workbench
Crystal structure of putative nag isomerase from salmonella typhimurium
Analyse Crystal structure of putative nag isomerase from salmonella typhimurium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AFA
- Type
- protein
- Length
- 2,448 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nag isomerase
- UniProt
- Q8ZKT7
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nag isomerase | protein | 408 | 50% helix, 10% strand | Q8ZKT7 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.80 | 0.81 | 155 | empty |
| 2 | 654 | 0.78 | 0.83 | 93 | empty |
| 3 | 59 | 0.72 | 0.98 | 19 | empty |
| 4 | 805 | 0.72 | 0.77 | 79 | empty |
| 5 | 53 | 0.72 | 0.99 | 20 | empty |
Interfaces
12 interfaces between chains.
- B–F · 658 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 656 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 651 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 644 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 641 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 modified (engineered).
Compared structures
- 2AFA · Crystal Structure of putative NAG isomerase from Salmonella typhimurium · the same entry in another collection · chain C against C, TM-score 1.00
- Q8ZKT7 · AlphaFold monomer V2.0 prediction for sulfoquinovose isomerase (Q8ZKT7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8ZKT7
- Elsewhere: RCSB PDB 2AFA · PDBe 2AFA · UniProt Q8ZKT7
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