MolNFT v1 · #117494 · protein
Crystal structure of GTFA/B complex
5E9T · Glycosyltransferase GTF1: “Crystal structure of GTFA/B complex”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.78). MolNFT v1 #117494 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5E9T
- Type
- protein
- Length
- 1,898 residues
- Chains
- 4
- 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
- MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glycosyltransferase GTF1 (EC 2.4.1.-) | protein | 503 | 31% helix, 27% strand | Q9AET5 |
| B | Glycosyltransferase-stabilizing protein GTF2 | protein | 447 | 27% helix, 25% strand | Q79T00 |
| D | Glycosyltransferase-stabilizing protein GTF2 | protein | 445 | 25% helix, 26% strand | Q79T00 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.78 | 0.81 | 97 | empty |
| 2 | 1142 | 0.75 | 0.78 | 84 | MG |
| 3 | 659 | 0.69 | 0.77 | 70 | empty |
| 4 | 259 | 0.65 | 0.83 | 31 | empty |
| 5 | 505 | 0.65 | 0.77 | 63 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1611 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1592 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1074 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 992 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 100 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 5E9T · Crystal structure of GtfA/B complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9AET5 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine-- peptide… · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q79T00 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine-- peptide… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 5E9T · PDBe 5E9T · UniProt Q9AET5 · UniProt Q79T00
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