Research workbench
(H-ALPHA2M)4 semiactivated I state
Analyse (H-ALPHA2M)4 semiactivated I state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O7N
- Type
- protein
- Length
- 5,370 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-2-macroglobulin
- UniProt
- P01023
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 15% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha-2-macroglobulin | protein | 1275 | 16% helix, 36% strand | P01023 |
| B, D | Alpha-2-macroglobulin | protein | 1410 | 14% helix, 24% strand | P01023 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 34 copies · chains A, C, B, D
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 | 853 | 0.84 | 0.86 | 86 | empty |
| 2 | 945 | 0.83 | 0.85 | 122 | empty |
| 3 | 549 | 0.83 | 0.89 | 70 | empty |
| 4 | 140 | 0.79 | 0.96 | 32 | empty |
| 5 | 311 | 0.79 | 0.89 | 48 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2363 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 674 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 672 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 236 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 232 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 7O7N · (h-alpha2M)4 semiactivated I state · the same entry in another collection · chain D against D, TM-score 1.00
- P01023 · AlphaFold monomer V2.0 prediction for alpha-2-macroglobulin (P01023) · a predicted model of the same protein · chain D against A, TM-score 0.84
- 2P9R · Human alpha2-macroglogulin is composed of multiple domains, as predicted by homology with… · a predicted model of the same protein · chain C against A, TM-score 0.08
- 2P9R · Human ALPHA2-macroglogulin is composed of multiple domains, as predicted by homology with… · a predicted model of the same protein · chain C against A, TM-score 0.08
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 P01023
- Elsewhere: RCSB PDB 7O7N · PDBe 7O7N · UniProt P01023
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