Research workbench
(H-ALPHA2M)4 plasmin-activated II state
Analyse (H-ALPHA2M)4 plasmin-activated II state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O7S
- Type
- protein
- Length
- 5,236 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-2-macroglobulin
- UniProt
- P01023
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 15% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-2-macroglobulin | protein | 1276 | 15% helix, 21% strand | P01023 |
| C | Alpha-2-macroglobulin | protein | 1277 | 15% helix, 25% strand | P01023 |
| D | Alpha-2-macroglobulin | protein | 1407 | 13% helix, 18% strand | P01023 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A
- MAN · alpha-D-mannopyranose · sugar
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 | 1163 | 0.87 | 0.88 | 128 | empty |
| 2 | 772 | 0.86 | 0.89 | 125 | empty |
| 3 | 669 | 0.85 | 0.89 | 111 | empty |
| 4 | 473 | 0.83 | 0.90 | 79 | empty |
| 5 | 390 | 0.82 | 0.90 | 77 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2850 Ų buried · 59 hydrogen bonds · protein-protein
- B–D · 1946 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 1317 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1248 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1104 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 29 glycan (disulfide, N-glycosylation).
Compared structures
- 7O7S · (h-alpha2M)4 plasmin-activated II 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 0.85
- 2P9R · Human ALPHA2-macroglogulin is composed of multiple domains, as predicted by homology with… · a predicted model of the same protein · chain B 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 B 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 7O7S · PDBe 7O7S · UniProt P01023
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