MolNFT v1 · #37557 · protein
Crystal structure of human insulin-degrading enzyme in complex with insulin B chain
2G56: “Crystal structure of human insulin-degrading enzyme in complex with insulin B chain”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #37557 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2G56
- Type
- protein
- Length
- 1,965 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Insulin
- EC
- 3.4.24.56
- UniProt
- Q5T5N2, P01308
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 964 | 44% helix, 20% strand | Q5T5N2 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 964 | 44% helix, 20% strand | Q5T5N2 |
| C | Insulin | protein | 18 | 0% helix, 17% strand | P01308 |
| D | Insulin | protein | 19 | 0% helix, 16% strand | P01308 |
Ligands and binding sites
- DIO · 1,4-diethylene dioxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.86 | 0.87 | 95 | empty |
| 2 | 1021 | 0.82 | 0.83 | 130 | empty |
| 3 | 923 | 0.81 | 0.83 | 110 | DIO |
| 4 | 584 | 0.76 | 0.83 | 58 | empty |
| 5 | 538 | 0.74 | 0.82 | 53 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1524 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1064 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 998 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2G56 · crystal structure of human insulin-degrading enzyme in complex with insulin B chain · 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 Q5T5N2
- Every structure of UniProt P01308
- Elsewhere: RCSB PDB 2G56 · PDBe 2G56 · UniProt Q5T5N2 · UniProt P01308
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