Research workbench
Crystal structure of endopeptidase-induced ALPHA2-macroglobulin
Analyse Crystal structure of endopeptidase-induced ALPHA2-macroglobulin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TAV
- Type
- protein
- Length
- 5,234 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-2-macroglobulin
- UniProt
- P01023
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-2-macroglobulin | protein | 1416 | 15% helix, 34% strand | P01023 |
| B | Alpha-2-macroglobulin | protein | 1273 | 16% helix, 34% strand | P01023 |
| C | Alpha-2-macroglobulin | protein | 1274 | 16% helix, 36% strand | P01023 |
| D | Alpha-2-macroglobulin | protein | 1271 | 16% helix, 35% strand | P01023 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 47 copies · chains A, C, B, D
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains 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 | 1042 | 0.78 | 0.80 | 104 | empty |
| 2 | 855 | 0.78 | 0.81 | 62 | empty |
| 3 | 553 | 0.75 | 0.82 | 57 | empty |
| 4 | 804 | 0.75 | 0.79 | 82 | empty |
| 5 | 88 | 0.74 | 0.96 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2417 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 2273 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1098 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1070 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 806 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 29 glycan (disulfide, N-glycosylation).
Compared structures
- 6TAV · Crystal structure of endopeptidase-induced alpha2-macroglobulin · the same entry in another collection · chain B against B, TM-score 1.00
- P01023 · AlphaFold monomer V2.0 prediction for alpha-2-macroglobulin (P01023) · a predicted model of the same protein · chain C against A, TM-score 0.66
- 2P9R · Human alpha2-macroglogulin is composed of multiple domains, as predicted by homology with… · a predicted model of the same protein · chain D 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 D 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 6TAV · PDBe 6TAV · UniProt P01023
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