Research workbench
X-ray crystal structure of tdp-vancosaminyltransferase gtfd as a complex with tdp and the natural substrate, desvancosaminyl vancomycin.
Analyse X-ray crystal structure of tdp-vancosaminyltransferase gtfd as a complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RRV
- Type
- protein
- Length
- 815 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase gtfd; Desvancosaminyl vancomycin
- UniProt
- Q9AFC7
- Ligands
- TYD, BGC, K
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyltransferase gtfd | protein | 401 | 46% helix, 13% strand | Q9AFC7 |
| B | Glycosyltransferase gtfd | protein | 400 | 45% helix, 14% strand | Q9AFC7 |
| C, D | Desvancosaminyl vancomycin | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, C, B, D
- K · Potassium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
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 | 886 | 0.86 | 0.88 | 91 | K, TYD, GOL, BGC |
| 2 | 813 | 0.86 | 0.88 | 88 | K, TYD, GOL, BGC |
| 3 | 478 | 0.66 | 0.78 | 54 | empty |
| 4 | 123 | 0.48 | 0.79 | 22 | empty |
| 5 | 80 | 0.41 | 0.79 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 802 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 789 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 620 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 2 glycan (nonstandard, glycosylation).
Compared structures
- 1RRV · X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9AFC7 · AlphaFold monomer V2.0 prediction for devancosaminyl-vancomycin vancosaminetransferase… · 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 Q9AFC7
- Elsewhere: RCSB PDB 1RRV · PDBe 1RRV · UniProt Q9AFC7
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