Research workbench
Crystal structure a of the angiotensin-1 converting enzyme N-domain in complex with a diprolyl inhibitor.
Analyse Crystal structure a 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
- 6EN5
- Type
- protein
- Length
- 2,433 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme
- EC
- 3.2.1.-, 3.4.15.1
- UniProt
- P12821
- Ligands
- BJ2, NAG, FUC, BMA, MAN, ZN, MG, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 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 | 605 | 62% helix, 3% strand | P12821 |
| B | Angiotensin-converting enzyme (EC 3.2.1.-, 3.4.15.1) | protein | 608 | 62% helix, 2% 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 | 614 | 62% helix, 3% strand | P12821 |
Ligands and binding sites
- BJ2 · (2~{S})-1-[(2~{S})-2-[[(1~{S})-1-[(2~{S})-1-[(2~{S})-2-azanyl-4-oxidanyl-4-oxidanylidene-butanoyl]pyrrolidin-2-yl]-2-oxidanyl-2-oxidanylidene-ethyl]amino]propanoyl]pyrrolidine-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 7 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 12 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 6 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, C
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · chains A
- PGE · Triethylene glycol · additive · chains A, B
- XPE · 3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol · additive · chains 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.87 | 0.88 | 112 | BJ2, MG, PEG, EDO |
| 2 | 1155 | 0.87 | 0.88 | 123 | BJ2, MG, PEG |
| 3 | 1138 | 0.87 | 0.88 | 116 | BJ2, MG, PEG, EDO |
| 4 | 582 | 0.86 | 0.91 | 67 | BJ2, MG |
| 5 | 282 | 0.78 | 0.90 | 31 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1046 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 293 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 116 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6EN5 · Crystal structure A of the Angiotensin-1 converting enzyme N-domain in complex with a… · 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 C 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 6EN5 · PDBe 6EN5 · UniProt P12821
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