Research workbench
Crystal structure of human insulin-degrading enzyme (ide) in complex with human B-type natriuretic peptide (bnp)
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
- 3N56
- Type
- protein
- Length
- 1,906 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Natriuretic peptides B
- EC
- 3.4.24.56
- UniProt
- P14735, P16860
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 951 | 45% helix, 20% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 951 | 44% helix, 20% strand | P14735 |
| C, D | Natriuretic peptides B | protein | 2 | 0% helix, 0% strand | P16860 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.79 | 0.81 | 139 | DIO |
| 2 | 1067 | 0.79 | 0.80 | 95 | empty |
| 3 | 716 | 0.74 | 0.80 | 100 | DIO |
| 4 | 397 | 0.67 | 0.80 | 41 | empty |
| 5 | 389 | 0.63 | 0.78 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–B · 864 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 169 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 166 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3N56 · Crystal Structure of human Insulin-degrading enzyme (IDE) in complex with human B-type… · the same entry in another collection · chain A 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 P16860
- Elsewhere: RCSB PDB 3N56 · PDBe 3N56 · UniProt P14735 · UniProt P16860
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