MolNFT v1 · #164106 · protein
Cryo-EM structure of yeast ALG6 in complex with 6AG9 Fab and DOL25-P- glc
6SNH · Dolichyl pyrophosphate MAN9GLCNAC2 alpha-1,3…: “Cryo-EM structure of yeast ALG6 in complex with 6AG9 Fab and DOL25-P- glc”. Electron microscopy, 1 ligand (LMH), 13 pockets (best druggability 0.76). MolNFT v1 #164106 on GenesisL1: 3D…
- PDB
- 6SNH
- Type
- protein
- Length
- 918 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dolichyl pyrophosphate MAN9GLCNAC2 alpha-1,3- glucosyltransferase; 6AG9 Fab heavy chain…
- EC
- 2.4.1.267
- UniProt
- Q12001
- Ligands
- LMH
- Pockets
- 13 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Dolichyl pyrophosphate MAN9GLCNAC2 alpha-1,3- glucosyltransferase (EC 2.4.1.267) | protein | 479 | 68% helix, 0% strand | Q12001 |
| H | 6AG9 Fab heavy chain | protein | 225 | 4% helix, 40% strand | — |
| L | 6AG9 Fab light chain | protein | 214 | 5% helix, 46% strand | — |
Ligands and binding sites
- LMH · glucosyl-dolichol phosphate · ligand · chains X, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.76 | 0.78 | 74 | LMH |
| 2 | 129 | 0.73 | 0.93 | 33 | empty |
| 3 | 123 | 0.71 | 0.91 | 26 | empty |
| 4 | 63 | 0.60 | 0.90 | 17 | empty |
| 5 | 160 | 0.51 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1750 Ų buried · 4 hydrogen bonds · protein-protein
- X–H · 768 Ų buried · 3 hydrogen bonds · protein-protein
- X–L · 390 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6SNH · Cryo-EM structure of yeast ALG6 in complex with 6AG9 Fab and Dol25-P-Glc · the same entry in another collection · chain X against X, TM-score 1.00
- Q12001 · AlphaFold monomer V2.0 prediction for dolichyl pyrophosphate MAN9GLCNAC2… · a predicted model of the same protein · chain X against A, TM-score 0.98
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 Q12001
- Elsewhere: RCSB PDB 6SNH · PDBe 6SNH · UniProt Q12001
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