MolNFT v1 · #53950 · protein
AP2 clathrin adaptor core in active complex with cargo peptides
2XA7 · Adaptor-related protein complex 2, alpha 2 subunit: “AP2 clathrin adaptor core in active complex with cargo peptides”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.76). MolNFT v1 #53950 on GenesisL1: 3D…
- PDB
- 2XA7
- Type
- protein
- Length
- 1,768 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adaptor-related protein complex 2, alpha 2 subunit; Ap-2 complex subunit beta; Ap-2…
- UniProt
- Q66HM2, P63010, P84092, P62743
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adaptor-related protein complex 2, alpha 2 subunit | protein | 613 | 71% helix, 1% strand | Q66HM2 |
| B | Ap-2 complex subunit beta | protein | 579 | 66% helix, 0% strand | P63010 |
| M | Ap-2 complex subunit mu, | protein | 428 | 16% helix, 38% strand | P84092 |
| P | TGN38 cargo peptide | protein | 6 | 0% helix, 33% strand | — |
| S | Ap-2 complex subunit sigma | protein | 142 | 42% helix, 26% strand | P62743 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, S, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.76 | 0.97 | 21 | empty |
| 2 | 527 | 0.75 | 0.83 | 53 | SO4 |
| 3 | 117 | 0.75 | 0.94 | 19 | empty |
| 4 | 448 | 0.74 | 0.83 | 45 | empty |
| 5 | 667 | 0.74 | 0.80 | 71 | empty |
Interfaces
7 interfaces between chains.
- B–M · 4225 Ų buried · 51 hydrogen bonds · protein-protein
- A–S · 2825 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1971 Ų buried · 26 hydrogen bonds · protein-protein
- M–P · 510 Ų buried · 6 hydrogen bonds · protein-protein
- B–S · 310 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2XA7 · AP2 clathrin adaptor core in active complex with cargo peptides · the same entry in another collection · chain S against S, 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 0.97
- 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 0.92
- 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 0.80
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 2XA7 · PDBe 2XA7 · UniProt Q66HM2 · UniProt P63010 · UniProt P84092 · UniProt P62743
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