Research workbench
Cryo-EM structure of the Ams1 and Nbr1 complex
Analyse Cryo-EM structure of the Ams1 and Nbr1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DD9
- Type
- protein
- Length
- 4,516 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Escherichia coli (strain K12); Schizosaccharomyces pombe (strain 972 / ATCC…
- Molecule
- Alpha-mannosidase,ZZ-type zinc finger-containing protein…
- EC
- 3.2.1.24
- UniProt
- Q9UT61, Q9P792, P0AEX9
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · resolution 2.4 · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Alpha-mannosidase,ZZ-type zinc finger-containing protein P35G2.11c,Maltose/maltodextrin-binding periplasmic protein (EC 3.2.1.24) | protein | 1129 | 26% helix, 29% strand | Q9UT61, Q9P792, P0AEX9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, C, E, G
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 | 1001 | 0.89 | 0.91 | 100 | empty |
| 2 | 991 | 0.89 | 0.91 | 101 | empty |
| 3 | 160 | 0.82 | 0.98 | 28 | empty |
| 4 | 158 | 0.81 | 0.97 | 31 | empty |
| 5 | 166 | 0.81 | 0.97 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–E · 2531 Ų buried · 32 hydrogen bonds · protein-protein
- C–G · 2523 Ų buried · 32 hydrogen bonds · protein-protein
- C–E · 2176 Ų buried · 28 hydrogen bonds · protein-protein
- A–G · 2175 Ų buried · 28 hydrogen bonds · protein-protein
- E–G · 1375 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7DD9 · Cryo-EM structure of the AMS1 and NBR1 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UT61 · AlphaFold monomer V2.0 prediction for alpha-mannosidase (Q9UT61) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q9P792 · AlphaFold monomer V2.0 prediction for zz-type zinc finger-containing protein P35G2.11C… · a predicted model of the same protein · chain A against A, TM-score 0.15
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 Q9UT61
- Every structure of UniProt Q9P792
- Every structure of UniProt P0AEX9
- Elsewhere: RCSB PDB 7DD9 · PDBe 7DD9 · UniProt Q9UT61 · UniProt Q9P792 · UniProt P0AEX9
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