Research workbench
AP2 clathrin adaptor core
Analyse AP2 clathrin adaptor core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VGL
- Type
- protein
- Length
- 1,717 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adaptor protein complex ap-2, alpha 2 subunit; Ap-2 complex subunit beta-1; Ap-2 complex…
- UniProt
- Q66HM2, P63010, P84092, P62743
- Ligands
- IHP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adaptor protein complex ap-2, alpha 2 subunit | protein | 600 | 73% helix, 1% strand | Q66HM2 |
| B | Ap-2 complex subunit beta-1 | protein | 579 | 63% helix, 0% strand | P63010 |
| M | Ap-2 complex subunit mu-1 | protein | 396 | 15% helix, 44% strand | P84092 |
| S | Ap-2 complex subunit sigma-1 | protein | 142 | 45% helix, 26% strand | P62743 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.84 | 0.85 | 99 | empty |
| 2 | 782 | 0.82 | 0.85 | 75 | empty |
| 3 | 967 | 0.81 | 0.83 | 86 | empty |
| 4 | 733 | 0.76 | 0.81 | 71 | empty |
| 5 | 412 | 0.69 | 0.81 | 43 | empty |
Interfaces
6 interfaces between chains.
- B–M · 3441 Ų buried · 37 hydrogen bonds · protein-protein
- A–S · 2465 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1898 Ų buried · 18 hydrogen bonds · protein-protein
- A–M · 1243 Ų buried · 9 hydrogen bonds · protein-protein
- B–S · 655 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2VGL · AP2 clathrin adaptor core · the same entry in another collection · chain A against A, TM-score 1.00
- P62743 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit sigma (P62743) · a predicted model of the same protein · chain S against A, TM-score 0.98
- P63010 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit beta (P63010) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P84092 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit mu (P84092) · a predicted model of the same protein · chain M against A, TM-score 0.60
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 Q66HM2
- Every structure of UniProt P63010
- Every structure of UniProt P84092
- Every structure of UniProt P62743
- Elsewhere: RCSB PDB 2VGL · PDBe 2VGL · UniProt Q66HM2 · UniProt P63010 · UniProt P84092 · UniProt P62743
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