Research workbench
Crystal structure of sugar aminotransferase CALS13 from micromonospora echinospora
Analyse Crystal structure of sugar aminotransferase CALS13 from micromonospora… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZAS
- Type
- protein
- Length
- 2,214 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALS13
- UniProt
- Q8KND8
- Ligands
- TYD, T46, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | CALS13 | protein | 369 | 39% helix, 16% strand | Q8KND8 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 3 copies · chains C, D, E, F
- T46 · dTDP-4-keto-6-deoxyglucose · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.78 | 0.80 | 103 | TYD |
| 2 | 90 | 0.77 | 0.98 | 23 | empty |
| 3 | 100 | 0.77 | 0.98 | 26 | empty |
| 4 | 91 | 0.77 | 0.98 | 24 | empty |
| 5 | 1070 | 0.76 | 0.79 | 105 | empty |
Interfaces
7 interfaces between chains.
- E–F · 2281 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2268 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2247 Ų buried · 45 hydrogen bonds · protein-protein
- D–F · 339 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 305 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (cofactor).
Compared structures
- 4ZAS · Crystal structure of sugar aminotransferase CalS13 from Micromonospora echinospora · 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 Q8KND8
- Elsewhere: RCSB PDB 4ZAS · PDBe 4ZAS · UniProt Q8KND8
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