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Crystal structure of tdp-epi-vancosaminyltransferase gtfa in complexes with tdp and the acceptor substrate dvv.
Analyse Crystal structure of tdp-epi-vancosaminyltransferase gtfa in complexes with tdp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PN3
- Type
- protein
- Length
- 789 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase gtfa; Desvancosaminyl vancomycin
- UniProt
- P96558
- Ligands
- TYD, BGC
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyltransferase gtfa | protein | 391 | 46% helix, 14% strand | P96558 |
| B | Glycosyltransferase gtfa | protein | 384 | 48% helix, 15% strand | P96558 |
| C, D | Desvancosaminyl vancomycin | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.81 | 0.83 | 89 | TYD, BGC |
| 2 | 735 | 0.77 | 0.81 | 76 | empty |
| 3 | 104 | 0.57 | 0.85 | 20 | empty |
| 4 | 84 | 0.56 | 0.86 | 23 | empty |
| 5 | 322 | 0.54 | 0.75 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 925 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 663 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 638 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 2 glycan (nonstandard, glycosylation).
Compared structures
- 1PN3 · Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and the… · 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 0.98
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 1PN3 · PDBe 1PN3 · UniProt P96558
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