Research workbench
Crystal structure of the angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 4-10
Analyse Crystal structure of the angiotensin-1 converting enzyme N-domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AM8
- Type
- protein
- Length
- 2,436 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme; Beta-amyloid protein 42
- EC
- 3.2.1.-, 3.4.15.1
- UniProt
- P12821, P05067
- Ligands
- NAG, FUC, BMA, FUL, MAN, ZN, CL, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 62% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme (EC 3.2.1.-, 3.4.15.1) | protein | 604 | 63% helix, 3% strand | P12821 |
| B | Angiotensin-converting enzyme (EC 3.2.1.-, 3.4.15.1) | protein | 606 | 62% helix, 3% strand | P12821 |
| C | Angiotensin-converting enzyme (EC 3.2.1.-, 3.4.15.1) | protein | 606 | 62% helix, 3% strand | P12821 |
| D | Angiotensin-converting enzyme (EC 3.2.1.-, 3.4.15.1) | protein | 612 | 62% helix, 2% strand | P12821 |
| P, Q, R, S | Beta-amyloid protein 42 | protein | 2 | 0% helix, 0% strand | P05067 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B, D, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains B, D, C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, C
- FUL · beta-L-fucopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar · chains D
- ZN · Zinc ion · metal · 4 copies · chains A, P, B, Q, C, R, D, S
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, P, B, Q, C, R, D, S
- PEG · Di(hydroxyethyl)ether · additive · 18 copies · chains A, C, B, D
- P6G · Hexaethylene glycol · additive · 3 copies · chains A, C, B, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.84 | 0.94 | 53 | SO4 |
| 2 | 832 | 0.83 | 0.86 | 78 | PEG |
| 3 | 803 | 0.83 | 0.86 | 73 | PEG |
| 4 | 777 | 0.83 | 0.86 | 77 | ZN, PEG |
| 5 | 460 | 0.82 | 0.90 | 72 | SO4 |
Interfaces
7 interfaces between chains.
- B–D · 1046 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 291 Ų buried · 2 hydrogen bonds · protein-protein
- B–Q · 245 Ų buried · 8 hydrogen bonds · protein-protein
- D–S · 243 Ų buried · 8 hydrogen bonds · protein-protein
- C–R · 243 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5AM8 · Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P12821 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme (P12821) · a predicted model of the same protein · chain A 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 5AM8 · PDBe 5AM8 · UniProt P12821 · UniProt P05067
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