MolNFT v1 · #73881 · protein
Crystal structure of human insulin-degrading enzyme in complex with ubiquitin
3OFI: “Crystal structure of human insulin-degrading enzyme in complex with ubiquitin”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.79). MolNFT v1 #73881 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OFI
- Type
- protein
- Length
- 1,914 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Ubiquitin
- EC
- 3.4.24.56
- UniProt
- P14735, P0CG48
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 954 | 44% helix, 20% strand | P14735 |
| C, D | Ubiquitin | protein | 3 | 0% helix, 33% strand | P0CG48 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · 3 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 | 1086 | 0.79 | 0.81 | 97 | empty |
| 2 | 1115 | 0.78 | 0.80 | 132 | empty |
| 3 | 647 | 0.71 | 0.79 | 86 | empty |
| 4 | 506 | 0.69 | 0.80 | 69 | DIO |
| 5 | 836 | 0.69 | 0.75 | 80 | DIO |
Interfaces
3 interfaces between chains.
- A–B · 926 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 323 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 309 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3OFI · Crystal structure of human insulin-degrading enzyme in complex with ubiquitin · 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 P0CG48
- Elsewhere: RCSB PDB 3OFI · PDBe 3OFI · UniProt P14735 · UniProt P0CG48
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