MolNFT v1 · #113669 · protein
Crystal structure of the angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 35-42
5AMB · Angiotensin-converting enzyme: “Crystal structure of the angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 35-42”. X-ray diffraction, 5 ligands (NAG, FUC, BMA), 12 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 5AMB
- Type
- protein
- Length
- 1,218 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme; Amyloid beta A4 protein
- EC
- 3.4.15.1
- UniProt
- P12821, P05067
- Ligands
- NAG, FUC, BMA, ZN, CL
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Angiotensin-converting enzyme (EC 3.4.15.1) | protein | 607 | 62% helix, 3% strand | P12821 |
| P, Q | Amyloid beta A4 protein | protein | 2 | 0% helix, 0% strand | P05067 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, P, B, Q
- CL · Chloride ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 870 | 0.84 | 0.86 | 76 | P6G |
| 2 | 1175 | 0.83 | 0.84 | 69 | P6G |
| 3 | 459 | 0.82 | 0.89 | 73 | empty |
| 4 | 441 | 0.81 | 0.89 | 73 | empty |
| 5 | 257 | 0.77 | 0.90 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1056 Ų buried · 14 hydrogen bonds · protein-protein
- A–P · 240 Ų buried · 8 hydrogen bonds · protein-protein
- B–Q · 239 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- P12821 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme (P12821) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P12821
- Every structure of UniProt P05067
- Elsewhere: RCSB PDB 5AMB · PDBe 5AMB · UniProt P12821 · UniProt P05067
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