Research workbench
Human angiotenisn converting enzyme N-domain in complex with phosphinic tripeptide
Analyse Human angiotenisn converting enzyme N-domain in complex with phosphinic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XYD
- Type
- protein
- Length
- 1,214 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme
- EC
- 3.4.15.1
- UniProt
- P12821
- Ligands
- 3ES, NAG, FUC, BMA, ZN, CL
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Angiotensin-converting enzyme (EC 3.4.15.1) | protein | 607 | 63% helix, 3% strand | P12821 |
Ligands and binding sites
- 3ES · [(2S)-2-({3-[hydroxyl(2-phenyl-(1R)-1-{[(benzyloxy)[(2s)-2-({3-[hydroxyl(2-phenyl-(1R)-1-carbonyl]-amino}ethyl)phosphinyl]-2-[(3-phenylisoxazol-5-yl)methyl]-1-oxo-propyl}amino)-3-(4-hydroxy-phenyl) · ligand · 2 copies · chains A, B
- 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, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- P6G · Hexaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.87 | 0.88 | 123 | 3ES, PEG |
| 2 | 494 | 0.85 | 0.91 | 51 | 3ES |
| 3 | 684 | 0.81 | 0.85 | 75 | 3ES, PEG |
| 4 | 258 | 0.76 | 0.89 | 34 | empty |
| 5 | 532 | 0.67 | 0.78 | 50 | PG4 |
Interfaces
1 interface between chains.
- A–B · 1014 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 2XYD · human Angiotenisn converting enzyme N-domain in complex with Phosphinic tripeptide · the same entry in another collection · chain B against B, TM-score 1.00
- 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
- Elsewhere: RCSB PDB 2XYD · PDBe 2XYD · UniProt P12821
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