Research workbench
Peptide-in-groove interactions link target proteins to the B-propeller of clathrin
Analyse Peptide-in-groove interactions link target proteins to the B-propeller of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C9I
- Type
- protein
- Length
- 726 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clathrin; B-adaptin 3
- UniProt
- P11442
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clathrin | protein | 355 | 8% helix, 51% strand | P11442 |
| B | Clathrin | protein | 355 | 8% helix, 52% strand | P11442 |
| C | B-adaptin 3 | protein | 9 | 0% helix, 11% strand | — |
| D | B-adaptin 3 | protein | 7 | 0% helix, 14% strand | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.82 | 0.83 | 99 | empty |
| 2 | 690 | 0.75 | 0.81 | 75 | empty |
| 3 | 66 | 0.31 | 0.75 | 16 | empty |
| 4 | 60 | 0.29 | 0.75 | 17 | empty |
| 5 | 52 | 0.29 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 827 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 505 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 500 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1C9I · Peptide-in-groove interactions link target proteins to the B-propeller of clathrin · the same entry in another collection · chain A against A, TM-score 1.00
- P11442 · AlphaFold monomer V2.0 prediction for clathrin heavy chain 1 (P11442) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P11442
- Elsewhere: RCSB PDB 1C9I · PDBe 1C9I · UniProt P11442
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