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
- 6BF9
- Type
- protein
- Length
- 2,743 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 0.85
Structure
electron microscopy · 5 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 948 | 41% helix, 15% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 940 | 41% helix, 16% strand | P14735 |
| C, E | Fab H11-E heavy chain | protein | 217 | 1% helix, 40% strand | P0DOX5 |
| D | Fab H11-E light chain | protein | 211 | 4% helix, 38% strand | P0DOX7 |
| F | Fab H11-E light chain | protein | 210 | 4% 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 | 855 | 0.85 | 0.87 | 73 | empty |
| 2 | 200 | 0.82 | 0.95 | 51 | empty |
| 3 | 1082 | 0.80 | 0.81 | 106 | empty |
| 4 | 396 | 0.80 | 0.88 | 87 | empty |
| 5 | 99 | 0.79 | 0.98 | 28 | empty |
Interfaces
7 interfaces between chains.
- E–F · 2219 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1755 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1392 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 733 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 718 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6BF9 · Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11-E heavy… · the same entry in another collection · chain F against F, 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 0.93
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 6BF9 · PDBe 6BF9 · UniProt P14735 · UniProt P0DOX5 · UniProt P0DOX7
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