MolNFT v1 · #117495 · protein
Crystal structure of GTFA/B complex bound to udp and glcnac
5E9U · Glycosyltransferase GTF1: “Crystal structure of GTFA/B complex bound to udp and glcnac”. X-ray diffraction, 3 ligands (UDP, NAG, MG), 20 pockets (best druggability 0.81). MolNFT v1 #117495 on GenesisL1: 3D structure, binding sites…
- PDB
- 5E9U
- Type
- protein
- Length
- 3,793 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase GTF1; Glycosyltransferase-stabilizing protein GTF2
- EC
- 2.4.1.-
- UniProt
- Q9AET5, Q79T00
- Ligands
- UDP, NAG, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Glycosyltransferase GTF1 (EC 2.4.1.-) | protein | 503 | 30% helix, 26% strand | Q9AET5 |
| B, F, H | Glycosyltransferase-stabilizing protein GTF2 | protein | 445 | 27% helix, 22% strand | Q79T00 |
| D | Glycosyltransferase-stabilizing protein GTF2 | protein | 446 | 26% helix, 26% strand | Q79T00 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, E
- MG · Magnesium ion · metal · 4 copies · chains B, C, A, D, E, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.81 | 0.86 | 78 | UDP, NAG |
| 2 | 649 | 0.78 | 0.83 | 79 | empty |
| 3 | 901 | 0.78 | 0.80 | 97 | empty |
| 4 | 663 | 0.78 | 0.83 | 56 | empty |
| 5 | 426 | 0.77 | 0.86 | 54 | UDP, NAG |
Interfaces
10 interfaces between chains.
- E–F · 1747 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1740 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1720 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1708 Ų buried · 24 hydrogen bonds · protein-protein
- F–G · 1269 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified (engineered).
Compared structures
- 5E9U · Crystal structure of GtfA/B complex bound to UDP and GlcNAc · the same entry in another collection · chain H against H, TM-score 1.00
- Q79T00 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine-- peptide… · a predicted model of the same protein · chain B against A, TM-score 0.95
- Q9AET5 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine-- peptide… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q9AET5
- Every structure of UniProt Q79T00
- Elsewhere: RCSB PDB 5E9U · PDBe 5E9U · UniProt Q9AET5 · UniProt Q79T00
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