MolNFT v1 · #138602 · protein
Crystal structure analysis of FAB1-bound human insulin degrading enzyme (ide) in complex with insulin
5WOB · Insulin-degrading enzyme: “Crystal structure analysis of FAB1-bound human insulin degrading enzyme (ide) in complex with insulin”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.88). MolNFT v1 #138602 on…
- PDB
- 5WOB
- Type
- protein
- Length
- 10,833 residues
- Chains
- 32
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Insulin; Ide-bound Fab heavy chain; Ide-bound Fab light chain
- EC
- 3.4.24.56
- UniProt
- P14735, P01308
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 30 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 941 | 42% helix, 20% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 947 | 43% helix, 20% strand | P14735 |
| C | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 950 | 43% helix, 20% strand | P14735 |
| D | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 952 | 43% helix, 20% strand | P14735 |
| E | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 943 | 42% helix, 20% strand | P14735 |
| F | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 944 | 42% helix, 19% strand | P14735 |
| G | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 943 | 41% helix, 20% strand | P14735 |
| H | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 936 | 43% helix, 21% strand | P14735 |
| a, c | Insulin | protein | 20 | 0% helix, 0% strand | P01308 |
| b | Insulin | protein | 5 | 0% helix, 0% strand | P01308 |
| d | Insulin | protein | 3 | 0% helix, 0% strand | P01308 |
| e | Insulin | protein | 9 | 0% helix, 0% strand | P01308 |
| f | Insulin | protein | 18 | 0% helix, 0% strand | P01308 |
| g | Insulin | protein | 15 | 0% helix, 7% strand | P01308 |
| h | Insulin | protein | 6 | 0% helix, 0% strand | P01308 |
| I, S | Ide-bound Fab heavy chain | protein | 215 | 1% helix, 50% strand | — |
| K | Ide-bound Fab heavy chain | protein | 207 | 0% helix, 48% strand | — |
| M | Ide-bound Fab heavy chain | protein | 214 | 1% helix, 50% strand | — |
| O | Ide-bound Fab heavy chain | protein | 209 | 1% helix, 45% strand | — |
| Q | Ide-bound Fab heavy chain | protein | 201 | 3% helix, 44% strand | — |
| U | Ide-bound Fab heavy chain | protein | 199 | 2% helix, 44% strand | — |
| W | Ide-bound Fab heavy chain | protein | 204 | 1% helix, 46% strand | — |
| J | Ide-bound Fab light chain | protein | 198 | 4% helix, 43% strand | — |
| L | Ide-bound Fab light chain | protein | 176 | 3% helix, 43% strand | — |
| N | Ide-bound Fab light chain | protein | 200 | 4% helix, 49% strand | — |
| P | Ide-bound Fab light chain | protein | 184 | 2% helix, 39% strand | — |
| R | Ide-bound Fab light chain | protein | 177 | 5% helix, 38% strand | — |
| T | Ide-bound Fab light chain | protein | 198 | 2% helix, 42% strand | — |
| V | Ide-bound Fab light chain | protein | 186 | 6% helix, 41% strand | — |
| X | Ide-bound Fab light chain | protein | 198 | 5% helix, 42% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, a, B, C, c, D, E, e, F, f, G, g, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 853 | 0.88 | 0.90 | 90 | empty |
| 2 | 1051 | 0.87 | 0.88 | 108 | empty |
| 3 | 1099 | 0.87 | 0.88 | 106 | empty |
| 4 | 1010 | 0.86 | 0.87 | 100 | empty |
| 5 | 1055 | 0.86 | 0.87 | 127 | empty |
Interfaces
44 interfaces between chains.
- O–P · 2022 Ų buried · 11 hydrogen bonds · protein-protein
- M–N · 2005 Ų buried · 9 hydrogen bonds · protein-protein
- S–T · 1980 Ų buried · 9 hydrogen bonds · protein-protein
- I–J · 1975 Ų buried · 8 hydrogen bonds · protein-protein
- W–X · 1946 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide (disulfide).
Compared structures
- 5WOB · Crystal Structure Analysis of Fab1-Bound Human Insulin Degrading Enzyme (IDE) in Complex… · the same entry in another collection · chain B against B, 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 5WOB · PDBe 5WOB · UniProt P14735 · UniProt P01308
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