Research workbench
Crystal structure of the fucosylgalactoside alpha N- acetylgalactosaminyltransferase (gta, cisab mutant L266G, G268A) in complex with a novel udp-gal derived inhibitor (5GW) and H-antigen acceptor
Analyse Crystal structure of the fucosylgalactoside alpha N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V0M
- Type
- protein
- Length
- 575 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histo-blood group abo system transferase
- EC
- 2.4.1.40, 2.4.1.37
- UniProt
- P16442
- Ligands
- 5GW, BHE, MN, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histo-blood group abo system transferase (EC 2.4.1.40, 2.4.1.37) | protein | 289 | 33% helix, 19% strand | P16442 |
| B | Histo-blood group abo system transferase (EC 2.4.1.40, 2.4.1.37) | protein | 286 | 32% helix, 19% strand | P16442 |
Ligands and binding sites
- 5GW · 5-phenyluridine 5'-(trihydrogen diphosphate) · ligand · 2 copies · chains A, B
- BHE · octyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.81 | 0.83 | 56 | empty |
| 2 | 398 | 0.66 | 0.79 | 40 | 5GW, BHE |
| 3 | 430 | 0.65 | 0.78 | 35 | MN, 5GW, BHE |
| 4 | 227 | 0.60 | 0.80 | 41 | empty |
| 5 | 55 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2807 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3V0M · Crystal structure of the Fucosylgalactoside alpha N-acetylgalactosaminyltransferase (GTA… · the same entry in another collection · chain A against A, TM-score 1.00
- P16442 · AlphaFold monomer V2.0 prediction for histo-blood group abo system transferase (P16442) · 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 P16442
- Elsewhere: RCSB PDB 3V0M · PDBe 3V0M · UniProt P16442
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