Research workbench
Crystal structure of AVIGT4, a glycosyltransferase involved in avilamycin a biosynthesis
Analyse Crystal structure of AVIGT4, a glycosyltransferase involved in avilamycin a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IV3
- Type
- protein
- Length
- 1,349 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase
- UniProt
- Q93KV2
- Ligands
- UDP
- Pockets
- 6 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyltransferase | protein | 337 | 36% helix, 17% strand | Q93KV2 |
| B | Glycosyltransferase | protein | 334 | 37% helix, 16% strand | Q93KV2 |
| C | Glycosyltransferase | protein | 340 | 37% helix, 17% strand | Q93KV2 |
| D | Glycosyltransferase | protein | 338 | 36% helix, 17% strand | Q93KV2 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.90 | 0.91 | 127 | UDP, GOL |
| 2 | 554 | 0.85 | 0.90 | 79 | UDP, GOL |
| 3 | 322 | 0.80 | 0.90 | 54 | UDP, GOL |
| 4 | 131 | 0.49 | 0.79 | 38 | empty |
| 5 | 57 | 0.43 | 0.82 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1246 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1099 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 405 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2IV3 · Crystal structure of AviGT4, a glycosyltransferase involved in Avilamycin A biosynthesis · 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 Q93KV2
- Elsewhere: RCSB PDB 2IV3 · PDBe 2IV3 · UniProt Q93KV2
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