Research workbench
AP2 on a membrane containing tyrosine-based cargo peptide
Analyse AP2 on a membrane containing tyrosine-based cargo peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YAF
- Type
- protein
- Length
- 1,768 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ap-2 complex subunit alpha-2; Ap-2 complex subunit beta; Ap-2 complex subunit mu…
- UniProt
- P18484, P63010, P84092, P62743
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ap-2 complex subunit alpha-2 | protein | 613 | 70% helix, 0% strand | P18484 |
| B | Ap-2 complex subunit beta | protein | 579 | 68% helix, 0% strand | P63010 |
| M | Ap-2 complex subunit mu | protein | 428 | 16% helix, 35% strand | P84092 |
| P | Tyrosine type cargo signal derived from TGN38 | protein | 6 | 0% helix, 0% strand | — |
| S | Ap-2 complex subunit sigma | protein | 142 | 45% helix, 20% strand | P62743 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.87 | 0.88 | 146 | empty |
| 2 | 1150 | 0.85 | 0.85 | 120 | empty |
| 3 | 1194 | 0.82 | 0.83 | 127 | empty |
| 4 | 301 | 0.79 | 0.89 | 52 | empty |
| 5 | 267 | 0.78 | 0.90 | 47 | empty |
Interfaces
7 interfaces between chains.
- B–M · 3069 Ų buried · 43 hydrogen bonds · protein-protein
- A–S · 1846 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1246 Ų buried · 22 hydrogen bonds · protein-protein
- M–P · 502 Ų buried · 10 hydrogen bonds · protein-protein
- B–S · 61 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6YAF · AP2 on a membrane containing tyrosine-based cargo peptide · 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 0.92
- 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 0.88
- P18484 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit alpha-2 (P18484) · a predicted model of the same protein · chain A against A, TM-score 0.88
- 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 0.82
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 P18484
- Every structure of UniProt P63010
- Every structure of UniProt P84092
- Every structure of UniProt P62743
- Elsewhere: RCSB PDB 6YAF · PDBe 6YAF · UniProt P18484 · UniProt P63010 · UniProt P84092 · UniProt P62743
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