Research workbench
Crystal structure of human insulin-degrading enzyme (ide) in complex with human atrial natriuretic peptide (anp)
Analyse Crystal structure of human insulin-degrading enzyme (ide) in complex with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N57
- Type
- protein
- Length
- 1,912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Atrial natriuretic factor
- EC
- 3.4.24.56
- UniProt
- P14735, P01160
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 953 | 45% helix, 20% strand | P14735 |
| C, D | Atrial natriuretic factor | protein | 3 | 0% helix, 33% strand | P01160 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.79 | 0.80 | 95 | empty |
| 2 | 872 | 0.76 | 0.80 | 95 | empty |
| 3 | 665 | 0.76 | 0.82 | 76 | ZN |
| 4 | 573 | 0.68 | 0.78 | 67 | empty |
| 5 | 402 | 0.67 | 0.80 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 861 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 319 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 314 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 3N57 · Crystal Structure of human Insulin-degrading enzyme (IDE) in complex with human atrial… · the same entry in another collection · chain A against A, TM-score 1.00
- P01160 · AlphaFold monomer V2.0 prediction for natriuretic peptides a (P01160) · a predicted model of the same protein · chain C against A, TM-score 1.00
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 P14735
- Every structure of UniProt P01160
- Elsewhere: RCSB PDB 3N57 · PDBe 3N57 · UniProt P14735 · UniProt P01160
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