MolNFT v1 · #183934 · protein
(H-ALPHA2M)4 plasmin-activated I state
7O7R · Alpha-2-macroglobulin: “(H-ALPHA2M)4 plasmin-activated I state”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.79). MolNFT v1 #183934 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7O7R
- Type
- protein
- Length
- 5,126 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-2-macroglobulin
- UniProt
- P01023
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 15% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha-2-macroglobulin | protein | 1285 | 16% helix, 26% strand | P01023 |
| B, D | Alpha-2-macroglobulin | protein | 1278 | 15% helix, 31% strand | P01023 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 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 | 156 | 0.79 | 0.96 | 40 | empty |
| 2 | 157 | 0.79 | 0.95 | 37 | empty |
| 3 | 178 | 0.79 | 0.93 | 32 | empty |
| 4 | 1059 | 0.78 | 0.80 | 113 | empty |
| 5 | 222 | 0.78 | 0.91 | 59 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2474 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2439 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1161 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1076 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1070 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 28 glycan (disulfide, N-glycosylation).
Compared structures
- 7O7R · (h-alpha2M)4 plasmin-activated I state · 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 B against A, TM-score 0.67
- 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 7O7R · PDBe 7O7R · UniProt P01023
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