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Molecular structure of a metal-independent bacterial glycosyltransferase that catalyzes the synthesis of histo-blood group a antigen
Analyse Molecular structure of a metal-independent bacterial glycosyltransferase that… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AYJ
- Type
- protein
- Length
- 935 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bogt - metal-independent glycosyltransferase
- EC
- 2.4.1.40
- UniProt
- A7LVT2
- Ligands
- BGC, GAL, FUC
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bogt - metal-independent glycosyltransferase (EC 2.4.1.40) | protein | 231 | 33% helix, 23% strand | A7LVT2 |
| B | Bogt - metal-independent glycosyltransferase (EC 2.4.1.40) | protein | 235 | 31% helix, 23% strand | A7LVT2 |
| C | Bogt - metal-independent glycosyltransferase (EC 2.4.1.40) | protein | 233 | 29% helix, 23% strand | A7LVT2 |
| D | Bogt - metal-independent glycosyltransferase (EC 2.4.1.40) | protein | 236 | 29% helix, 22% strand | A7LVT2 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.79 | 0.80 | 78 | BGC, GAL, FUC |
| 2 | 813 | 0.77 | 0.80 | 74 | BGC, GAL, FUC |
| 3 | 1159 | 0.76 | 0.78 | 101 | empty |
| 4 | 69 | 0.67 | 0.94 | 24 | empty |
| 5 | 60 | 0.63 | 0.93 | 25 | empty |
Interfaces
6 interfaces between chains.
- B–C · 451 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 444 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 393 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 390 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 240 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (glycation).
Compared structures
- 4AYJ · Molecular structure of a metal-independent bacterial glycosyltransferase that catalyzes… · the same entry in another collection · chain A against A, TM-score 1.00
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 A7LVT2
- Elsewhere: RCSB PDB 4AYJ · PDBe 4AYJ · UniProt A7LVT2
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