Research workbench
Crystal structure analysis of elbow-engineered-Fab-bound human insulin degrading enzyme (ide) in complex with insulin
Analyse Crystal structure analysis of elbow-engineered-Fab-bound human insulin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CJO
- Type
- protein
- Length
- 1,371 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Fab heavy chain with engineered elbow; Fab light chain; Insulin
- EC
- 3.4.24.56
- UniProt
- P14735, P01308
- Ligands
- ZN
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 959 | 42% helix, 20% strand | P14735 |
| H | Fab heavy chain with engineered elbow | protein | 215 | 3% helix, 44% strand | — |
| L | Fab light chain | protein | 190 | 2% helix, 42% strand | — |
| a | Insulin | protein | 7 | 0% helix, 14% strand | P01308 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, a
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.78 | 0.80 | 120 | EPE |
| 2 | 899 | 0.77 | 0.80 | 104 | empty |
| 3 | 368 | 0.65 | 0.80 | 46 | empty |
| 4 | 349 | 0.54 | 0.74 | 51 | empty |
| 5 | 225 | 0.53 | 0.77 | 33 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1951 Ų buried · 14 hydrogen bonds · protein-protein
- A–a · 692 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 586 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5CJO · Crystal Structure Analysis of Elbow-Engineered-Fab-Bound Human Insulin Degrading Enzyme… · 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 P01308
- Elsewhere: RCSB PDB 5CJO · PDBe 5CJO · UniProt P14735 · UniProt P01308
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