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Crystal structure of ide-bradykinin complex
Analyse Crystal structure of ide-bradykinin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CWW
- Type
- protein
- Length
- 1,913 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Bradykinin N-terminal tetrapeptide analogue
- EC
- 3.4.24.56
- UniProt
- P14735
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 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 | 953 | 44% helix, 20% strand | P14735 |
| D | Bradykinin N-terminal tetrapeptide analogue | protein | 4 | 0% helix, 0% strand | — |
| E | Bradykinin N-terminal tetrapeptide analogue | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · 4 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.79 | 0.80 | 93 | empty |
| 2 | 593 | 0.75 | 0.82 | 85 | empty |
| 3 | 597 | 0.69 | 0.78 | 76 | DIO |
| 4 | 423 | 0.68 | 0.80 | 44 | empty |
| 5 | 395 | 0.64 | 0.78 | 57 | empty |
Interfaces
3 interfaces between chains.
- A–B · 907 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 234 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 229 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3CWW · Crystal Structure of IDE-bradykinin complex · 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
- Elsewhere: RCSB PDB 3CWW · PDBe 3CWW · UniProt P14735
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