Research workbench
AP2 clathrin adaptor core with two cargo peptides in open+ conformation
Analyse AP2 clathrin adaptor core with two cargo peptides in open+ conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QH6
- Type
- protein
- Length
- 1,671 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ap-2 complex subunit alpha; Ap-2 complex subunit beta; Ap-2 complex subunit mu; TGN38…
- UniProt
- Q66HM2, P63010, Q3ZC13, P84092, P62743
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ap-2 complex subunit alpha | protein | 614 | 72% helix, 0% strand | Q66HM2 |
| B | Ap-2 complex subunit beta | protein | 502 | 67% helix, 0% strand | P63010 |
| M | Ap-2 complex subunit mu | protein | 255 | 0% helix, 52% strand | Q3ZC13 |
| N | Ap-2 complex subunit mu | protein | 143 | 32% helix, 22% strand | P84092 |
| P | TGN38 cargo peptide | protein | 6 | 0% helix, 33% strand | — |
| Q | CD4 cargo peptide | protein | 9 | 0% helix, 11% strand | — |
| S | Ap-2 complex subunit sigma | protein | 142 | 43% helix, 27% strand | P62743 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.82 | 0.96 | 33 | empty |
| 2 | 288 | 0.77 | 0.89 | 42 | empty |
| 3 | 788 | 0.75 | 0.80 | 81 | empty |
| 4 | 607 | 0.75 | 0.81 | 51 | empty |
| 5 | 771 | 0.70 | 0.76 | 87 | empty |
Interfaces
9 interfaces between chains.
- A–S · 2827 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2008 Ų buried · 25 hydrogen bonds · protein-protein
- B–N · 1934 Ų buried · 31 hydrogen bonds · protein-protein
- B–M · 754 Ų buried · 6 hydrogen bonds · protein-protein
- Q–S · 506 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6QH6 · AP2 clathrin adaptor core with two cargo peptides in open+ conformation · 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 0.98
- Q3ZC13 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit mu (Q3ZC13) · a predicted model of the same protein · chain M against A, TM-score 0.95
- P84092 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit mu (P84092) · a predicted model of the same protein · chain N 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 0.79
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 Q3ZC13
- Every structure of UniProt P84092
- Every structure of UniProt P62743
- Elsewhere: RCSB PDB 6QH6 · PDBe 6QH6 · UniProt Q66HM2 · UniProt P63010 · UniProt Q3ZC13 · UniProt P84092 · UniProt P62743
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.