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Human meprin alpha inhibitory complex with compound 10d (N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide)
Analyse Human meprin alpha inhibitory complex with compound 10d… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UAF
- Type
- protein
- Length
- 2,131 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Homo sapiens
- Molecule
- Meprin A subunit alpha
- EC
- 3.4.24.18
- UniProt
- Q16819
- Ligands
- M6X, NAG, BMA, FUC, CA, ZN
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · resolution 2.4 · 3 distinct chains · 17% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Meprin A subunit alpha (EC 3.4.24.18) | protein | 535 | 17% helix, 33% strand | Q16819 |
| C | Meprin A subunit alpha (EC 3.4.24.18) | protein | 532 | 17% helix, 33% strand | Q16819 |
| D | Meprin A subunit alpha (EC 3.4.24.18) | protein | 529 | 16% helix, 33% strand | Q16819 |
Ligands and binding sites
- M6X · N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide · ligand · 4 copies · chains B, A, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 34 copies · chains B, A, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, A, C, D
- CA · Calcium ion · metal · 8 copies · chains B, A, C, D
- ZN · Zinc ion · metal · 4 copies · chains B, A, C, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.78 | 0.80 | 92 | empty |
| 2 | 665 | 0.77 | 0.83 | 57 | empty |
| 3 | 763 | 0.76 | 0.81 | 80 | empty |
| 4 | 701 | 0.76 | 0.81 | 61 | empty |
| 5 | 640 | 0.76 | 0.82 | 56 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1591 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1378 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1352 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- Q16819 · AlphaFold monomer V2.0 prediction for meprin a subunit alpha (Q16819) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q16819
- Elsewhere: RCSB PDB 7UAF · PDBe 7UAF · UniProt Q16819
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