Research workbench
AP2 core in physiological buffer
Analyse AP2 core in physiological buffer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YAE
- Type
- protein
- Length
- 1,717 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ap-2 complex subunit alpha; Ap-2 complex subunit beta; Ap-2 complex subunit mu; Ap-2…
- UniProt
- Q66HM2, P63010, P84092, P62743
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ap-2 complex subunit alpha | protein | 600 | 72% helix, 1% strand | Q66HM2 |
| B | Ap-2 complex subunit beta | protein | 579 | 66% helix, 0% strand | P63010 |
| M | Ap-2 complex subunit mu | protein | 396 | 13% helix, 45% strand | P84092 |
| S | Ap-2 complex subunit sigma | protein | 142 | 42% helix, 25% strand | P62743 |
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 | 823 | 0.82 | 0.85 | 77 | empty |
| 2 | 1062 | 0.80 | 0.82 | 109 | empty |
| 3 | 638 | 0.80 | 0.85 | 79 | empty |
| 4 | 435 | 0.76 | 0.85 | 51 | empty |
| 5 | 634 | 0.72 | 0.79 | 52 | empty |
Interfaces
6 interfaces between chains.
- B–M · 3290 Ų buried · 18 hydrogen bonds · protein-protein
- A–S · 2512 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1658 Ų buried · 23 hydrogen bonds · protein-protein
- A–M · 1146 Ų buried · 6 hydrogen bonds · protein-protein
- B–S · 726 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6YAE · AP2 core in physiological buffer · 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 6YAE · PDBe 6YAE · UniProt Q66HM2 · UniProt P63010 · UniProt P84092 · UniProt P62743
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