Research workbench
Cryo-EM structure of nanodisc reconstituted yeast ALG6 in complex with 6AG9 Fab
Analyse Cryo-EM structure of nanodisc reconstituted yeast ALG6 in complex with 6AG9 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SNI
- 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
- PTY, Y01
- Pockets
- 11 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Dolichyl pyrophosphate MAN9GLCNAC2 alpha-1,3- glucosyltransferase (EC 2.4.1.267) | protein | 479 | 64% helix, 0% strand | Q12001 |
| H | 6AG9-Fab heavy chain | protein | 225 | 5% helix, 46% strand | — |
| L | 6AG9-Fab light chain | protein | 214 | 6% helix, 48% strand | — |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 5 copies · chains X
- Y01 · Cholesterol hemisuccinate · ligand · 3 copies · chains X, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.76 | 0.78 | 60 | Y01 |
| 2 | 116 | 0.74 | 0.94 | 26 | empty |
| 3 | 103 | 0.62 | 0.88 | 21 | empty |
| 4 | 195 | 0.54 | 0.78 | 30 | empty |
| 5 | 300 | 0.51 | 0.74 | 49 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1840 Ų buried · 5 hydrogen bonds · protein-protein
- X–H · 817 Ų buried · 8 hydrogen bonds · protein-protein
- X–L · 437 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6SNI · Cryo-EM structure of nanodisc reconstituted yeast ALG6 in complex with 6AG9 Fab · 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 6SNI · PDBe 6SNI · UniProt Q12001
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