MolNFT v1 · #88053 · protein
Monoclinic crystal form of BOGT6A E192Q in complex with udp-galnac, udp and galnac
4CJ8 · Glycosyltransferase family 6: “Monoclinic crystal form of BOGT6A E192Q in complex with udp-galnac, udp and galnac”. X-ray diffraction, 5 ligands (UDP, UD2, A2G), 20 pockets (best druggability 0.83). MolNFT v1 #88053 on GenesisL1: 3D…
- PDB
- 4CJ8
- Type
- protein
- Length
- 3,852 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase family 6
- EC
- 2.4.1.40
- UniProt
- A7LVT2
- Ligands
- UDP, UD2, A2G, NGA, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 238 | 31% helix, 24% strand | A7LVT2 |
| D, K | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 237 | 30% helix, 24% strand | A7LVT2 |
| E, F, G | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 246 | 28% helix, 23% strand | A7LVT2 |
| H | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 247 | 28% helix, 21% strand | A7LVT2 |
| I, J, L | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 236 | 33% helix, 21% strand | A7LVT2 |
| M | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 245 | 29% helix, 22% strand | A7LVT2 |
| N, P | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 243 | 26% helix, 23% strand | A7LVT2 |
| O | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 240 | 28% helix, 22% strand | A7LVT2 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 10 copies · chains A, I, B, J, C, D, K, L, M, N
- UD2 · Uridine-diphosphate-N-acetylgalactosamine · ligand · 6 copies · chains E, F, G, H, O, P
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 8 copies · chains A, B, C, D, I, J, K, L
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains M, N
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 5 copies · chains A, I, D, G
- 1PE · Pentaethylene glycol · additive · chains A
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 | 1044 | 0.83 | 0.84 | 99 | UDP, A2G |
| 2 | 1105 | 0.83 | 0.84 | 87 | empty |
| 3 | 780 | 0.83 | 0.85 | 78 | empty |
| 4 | 706 | 0.81 | 0.85 | 70 | UD2 |
| 5 | 1151 | 0.81 | 0.82 | 83 | empty |
Interfaces
36 interfaces between chains.
- A–I · 654 Ų buried · 4 hydrogen bonds · protein-protein
- D–K · 635 Ų buried · 0 hydrogen bonds · protein-protein
- I–P · 578 Ų buried · 6 hydrogen bonds · protein-protein
- L–N · 564 Ų buried · 4 hydrogen bonds · protein-protein
- K–M · 563 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (glycosylation).
Compared structures
- 4CJ8 · monoclinic crystal form of Bogt6a E192Q in complex with UDP-GalNAc, UDP and GalNAc · the same entry in another collection · chain G against G, 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 4CJ8 · PDBe 4CJ8 · UniProt A7LVT2
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