Research workbench
Structure of tev cleaved A2ML1 dimer (A2ML1-tt dimer)
Analyse Structure of tev cleaved A2ML1 dimer (A2ML1-tt dimer) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q62
- Type
- protein
- Length
- 2,045 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-2-macroglobulin-like protein 1
- UniProt
- A8K2U0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-2-macroglobulin-like protein 1 | protein | 1223 | 15% helix, 39% strand | A8K2U0 |
| B | Alpha-2-macroglobulin-like protein 1 | protein | 822 | 3% helix, 51% strand | A8K2U0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.82 | 0.84 | 103 | empty |
| 2 | 88 | 0.74 | 0.96 | 23 | empty |
| 3 | 366 | 0.70 | 0.82 | 43 | empty |
| 4 | 593 | 0.68 | 0.77 | 66 | empty |
| 5 | 59 | 0.66 | 0.94 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1294 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 7Q62 · Structure of TEV cleaved A2ML1 dimer (A2ML1-TT dimer) · the same entry in another collection · chain A against A, TM-score 1.00
- A8K2U0 · AlphaFold monomer V2.0 prediction for alpha-2-macroglobulin-like protein 1 (A8K2U0) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 A8K2U0
- Elsewhere: RCSB PDB 7Q62 · PDBe 7Q62 · UniProt A8K2U0
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