Research workbench
Cryo-EM structure of human insulin degrading enzyme in complex with Fab H11-E heavy chain, Fab H11-E light chain
Analyse Cryo-EM structure of human insulin degrading enzyme in complex with Fab H11-E… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BF7
- Type
- protein
- Length
- 2,745 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Fab H11-E heavy chain; Fab H11-E light chain
- EC
- 3.4.24.56
- UniProt
- P14735, P0DOX5, P0DOX7
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 949 | 41% helix, 16% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 940 | 40% helix, 17% strand | P14735 |
| C, E | Fab H11-E heavy chain | protein | 217 | 1% helix, 46% strand | P0DOX5 |
| D, F | Fab H11-E light chain | protein | 211 | 3% helix, 45% strand | P0DOX7 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.87 | 0.88 | 115 | empty |
| 2 | 362 | 0.85 | 0.93 | 67 | empty |
| 3 | 427 | 0.85 | 0.92 | 76 | empty |
| 4 | 419 | 0.84 | 0.92 | 70 | empty |
| 5 | 343 | 0.79 | 0.89 | 60 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1799 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1778 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1203 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 832 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 782 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6BF7 · Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11-E heavy… · the same entry in another collection · chain C against C, TM-score 1.00
- P0DOX7 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa light chain (P0DOX7) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 P0DOX5
- Every structure of UniProt P0DOX7
- Elsewhere: RCSB PDB 6BF7 · PDBe 6BF7 · UniProt P14735 · UniProt P0DOX5 · UniProt P0DOX7
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