Research workbench
Cryo-EM structure of human glcnac-1-phosphotransferase A2B2 subcomplex
Analyse Cryo-EM structure of human glcnac-1-phosphotransferase A2B2 subcomplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S05
- Type
- protein
- Length
- 874 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosamine-1-phosphotransferase subunits ALPHA/BETA
- EC
- 2.7.8.17
- UniProt
- Q3T906
- Ligands
- NAG, CA
- Pockets
- 10 · best druggability 0.70
Structure
electron microscopy · 1 distinct chain · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | N-acetylglucosamine-1-phosphotransferase subunits ALPHA/BETA (EC 2.7.8.17) | protein | 437 | 44% helix, 14% strand | Q3T906 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains B, A
- CA · Calcium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.70 | 0.78 | 60 | empty |
| 2 | 690 | 0.70 | 0.77 | 60 | empty |
| 3 | 332 | 0.66 | 0.81 | 45 | empty |
| 4 | 217 | 0.61 | 0.81 | 35 | empty |
| 5 | 286 | 0.61 | 0.79 | 47 | empty |
Interfaces
1 interface between chains.
- B–A · 3259 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 7S05 · Cryo-EM structure of human GlcNAc-1-phosphotransferase A2B2 subcomplex · the same entry in another collection · chain B against B, TM-score 1.00
- Q3T906 · AlphaFold monomer V2.0 prediction for N-acetylglucosamine-1-phosphotransferase subunits… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q3T906
- Elsewhere: RCSB PDB 7S05 · PDBe 7S05 · UniProt Q3T906
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