MolNFT v1 · #183929 · protein
(H-ALPHA2M)4 native II
7O7M · Alpha-2-macroglobulin: “(H-ALPHA2M)4 native II”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.88). MolNFT v1 #183929 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7O7M
- Type
- protein
- Length
- 5,640 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 0.88
Structure
electron microscopy · 1 distinct chain · 13% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha-2-macroglobulin | protein | 1410 | 13% helix, 24% strand | P01023 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains B, D, A, C
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
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 | 1013 | 0.88 | 0.89 | 141 | empty |
| 2 | 1181 | 0.86 | 0.87 | 147 | empty |
| 3 | 1103 | 0.86 | 0.87 | 118 | empty |
| 4 | 1083 | 0.86 | 0.87 | 115 | empty |
| 5 | 661 | 0.86 | 0.90 | 93 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1002 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 996 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 653 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 652 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 451 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 7O7M · (h-alpha2M)4 native II · 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 C against A, TM-score 0.07
- 2P9R · Human alpha2-macroglogulin is composed of multiple domains, as predicted by homology with… · a predicted model of the same protein · chain A against A, TM-score 0.07
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 7O7M · PDBe 7O7M · UniProt P01023
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.