MolNFT v1 · #46283 · protein
Crystal structure of ALPHA1,3-fucosyltransferase with GDP-fucose
2NZY: “Crystal structure of ALPHA1,3-fucosyltransferase with GDP-fucose”. X-ray diffraction, 3 ligands (GDP, FUC, SO4), 17 pockets (best druggability 0.71). MolNFT v1 #46283 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2NZY
- Type
- protein
- Length
- 1,032 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALPHA1,3-fucosyltransferase
- EC
- 2.4.1.152
- UniProt
- O30511
- Ligands
- GDP, FUC, SO4
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ALPHA1,3-fucosyltransferase (EC 2.4.1.152) | protein | 343 | 36% helix, 16% strand | O30511 |
| B | ALPHA1,3-fucosyltransferase (EC 2.4.1.152) | protein | 338 | 37% helix, 17% strand | O30511 |
| C | ALPHA1,3-fucosyltransferase (EC 2.4.1.152) | protein | 351 | 39% helix, 16% strand | O30511 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.71 | 0.80 | 37 | empty |
| 2 | 450 | 0.70 | 0.81 | 56 | empty |
| 3 | 214 | 0.64 | 0.83 | 36 | empty |
| 4 | 268 | 0.56 | 0.77 | 39 | FUC, GDP |
| 5 | 193 | 0.55 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 958 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 789 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 389 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2NZY · Crystal Structure of alpha1,3-Fucosyltransferase with GDP-fucose · the same entry in another collection · chain A against A, TM-score 1.00
- O30511 · AlphaFold monomer V2.0 prediction for alpha-(1,3)-fucosyltransferase fuct (O30511) · a predicted model of the same protein · chain B 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 O30511
- Elsewhere: RCSB PDB 2NZY · PDBe 2NZY · UniProt O30511
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