MolNFT v1 · #37724 · protein
X-ray crystal structure of murine leukocyte-type core 2 B1,6-N- acetylglucosaminyltransferase (C2GNT-L)
2GAK · Beta-1,6-N-acetylglucosaminyltransferase: “X-ray crystal structure of murine leukocyte-type core 2 B1,6-N- acetylglucosaminyltransferase (C2GNT-L)”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 2GAK
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-1,6-N-acetylglucosaminyltransferase
- EC
- 2.4.1.102
- UniProt
- Q09324
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-1,6-N-acetylglucosaminyltransferase (EC 2.4.1.102) | protein | 374 | 41% helix, 16% strand | Q09324 |
| B | Beta-1,6-N-acetylglucosaminyltransferase (EC 2.4.1.102) | protein | 364 | 39% helix, 17% strand | Q09324 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.79 | 0.81 | 81 | empty |
| 2 | 717 | 0.74 | 0.79 | 63 | empty |
| 3 | 582 | 0.72 | 0.80 | 48 | empty |
| 4 | 64 | 0.58 | 0.90 | 26 | empty |
| 5 | 94 | 0.35 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1007 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2GAK · X-ray crystal structure of murine leukocyte-type Core 2… · the same entry in another collection · chain A against A, TM-score 1.00
- Q09324 · AlphaFold monomer V2.0 prediction for beta-1,3-galactosyl-O-glycosyl- glycoprotein… · a predicted model of the same protein · 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 Q09324
- Elsewhere: RCSB PDB 2GAK · PDBe 2GAK · UniProt Q09324
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