Research workbench
AP2 clathrin adaptor MU2T156-phosphorylated core with two cargo peptides in open+ conformation
Analyse AP2 clathrin adaptor MU2T156-phosphorylated core with two cargo peptides in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QH7
- 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; Adaptor-related protein complex 2…
- UniProt
- Q66HM2, P63010, Q3ZC13, P62743
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ap-2 complex subunit alpha | protein | 614 | 73% helix, 0% strand | Q66HM2 |
| B | Ap-2 complex subunit beta | protein | 502 | 67% helix, 0% strand | P63010 |
| M | Adaptor-related protein complex 2, mu 2 subunit, C-terminal domain | protein | 255 | 0% helix, 52% strand | Q3ZC13 |
| N | Adaptor-related protein complex 2, mu 2 subunit, C-terminal domain | protein | 143 | 32% helix, 22% strand | Q3ZC13 |
| P | TGN38 cargo peptide | protein | 6 | 0% helix, 33% strand | — |
| Q | CD4 cargo peptide | protein | 9 | 0% helix, 0% strand | — |
| S | Ap-2 complex subunit sigma | protein | 142 | 43% helix, 26% strand | P62743 |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.82 | 0.97 | 31 | empty |
| 2 | 730 | 0.80 | 0.84 | 89 | empty |
| 3 | 886 | 0.75 | 0.79 | 91 | empty |
| 4 | 622 | 0.74 | 0.81 | 53 | empty |
| 5 | 1108 | 0.73 | 0.76 | 118 | empty |
Interfaces
9 interfaces between chains.
- A–S · 2730 Ų buried · 35 hydrogen bonds · protein-protein
- B–N · 1930 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1914 Ų buried · 28 hydrogen bonds · protein-protein
- B–M · 757 Ų buried · 9 hydrogen bonds · protein-protein
- Q–S · 529 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6QH7 · AP2 clathrin adaptor mu2T156-phosphorylated core with two cargo peptides in open+… · 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
- 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 P62743
- Elsewhere: RCSB PDB 6QH7 · PDBe 6QH7 · UniProt Q66HM2 · UniProt P63010 · UniProt Q3ZC13 · UniProt P62743
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