MolNFT v1 · #18402 · protein
Crystal structure of tdp-epi-vancosaminyltransferase gtfa in complexes with tdp and vancomycin
1PNV · Glycosyltransferase gtfa: “Crystal structure of tdp-epi-vancosaminyltransferase gtfa in complexes with tdp and vancomycin”. X-ray diffraction, 3 ligands (RER, TYD, BGC), 8 pockets (best druggability 0.79). MolNFT v1 #18402 on…
- PDB
- 1PNV
- Type
- protein
- Length
- 773 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase gtfa; Vancomycin
- UniProt
- P96558
- Ligands
- RER, TYD, BGC
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyltransferase gtfa | protein | 382 | 47% helix, 14% strand | P96558 |
| B | Glycosyltransferase gtfa | protein | 384 | 46% helix, 14% strand | P96558 |
| C | Vancomycin | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- RER · vancosamine · ligand · chains B, C
- TYD · Thymidine-5'-diphosphate · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.79 | 0.81 | 96 | empty |
| 2 | 709 | 0.77 | 0.82 | 74 | TYD |
| 3 | 88 | 0.51 | 0.83 | 18 | empty |
| 4 | 267 | 0.51 | 0.75 | 34 | empty |
| 5 | 66 | 0.43 | 0.82 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 854 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 611 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 1 glycan (nonstandard, glycosylation).
Compared structures
- 1PNV · Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and… · the same entry in another collection · chain A against A, TM-score 1.00
- P96558 · AlphaFold monomer V2.0 prediction for dtdp-epi- vancosaminyltransferase (P96558) · 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 P96558
- Elsewhere: RCSB PDB 1PNV · PDBe 1PNV · UniProt P96558
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