Research workbench
Cryo-EM structure of phosphorylated ap-2 core bound to necap
Analyse Cryo-EM structure of phosphorylated ap-2 core bound to necap in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OWO
- Type
- protein
- Length
- 1,786 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; Ap-2…
- UniProt
- Q9DBG3, P84091, P62744, Q9D1J1
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ap-2 complex subunit alpha-2 | protein | 569 | 72% helix, 0% strand | — |
| B | Ap-2 complex subunit beta | protein | 559 | 69% helix, 0% strand | Q9DBG3 |
| M | Ap-2 complex subunit mu | protein | 395 | 12% helix, 46% strand | P84091 |
| S | Ap-2 complex subunit sigma | protein | 141 | 40% helix, 26% strand | P62744 |
| N | Adaptin ear-binding coat-associated protein 2 | protein | 122 | 20% helix, 39% strand | Q9D1J1 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.83 | 0.86 | 85 | empty |
| 2 | 646 | 0.81 | 0.86 | 59 | empty |
| 3 | 1159 | 0.80 | 0.81 | 98 | empty |
| 4 | 354 | 0.76 | 0.87 | 43 | empty |
| 5 | 708 | 0.75 | 0.81 | 81 | empty |
Interfaces
8 interfaces between chains.
- B–M · 3339 Ų buried · 37 hydrogen bonds · protein-protein
- A–S · 2418 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1351 Ų buried · 21 hydrogen bonds · protein-protein
- A–M · 1158 Ų buried · 16 hydrogen bonds · protein-protein
- M–N · 884 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6OWO · Cryo-EM structure of phosphorylated ap-2 core bound to necap · the same entry in another collection · chain N against N, TM-score 1.00
- P62744 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit sigma (P62744) · a predicted model of the same protein · chain S against A, TM-score 0.98
- Q9D1J1 · AlphaFold monomer V2.0 prediction for adaptin ear-binding coat- associated protein 2… · a predicted model of the same protein · chain N against A, TM-score 0.96
- Q9DBG3 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit beta (Q9DBG3) · a predicted model of the same protein · chain B against A, TM-score 0.93
- P84091 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit mu (P84091) · 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 Q9DBG3
- Every structure of UniProt P84091
- Every structure of UniProt P62744
- Every structure of UniProt Q9D1J1
- Elsewhere: RCSB PDB 6OWO · PDBe 6OWO · UniProt Q9DBG3 · UniProt P84091 · UniProt P62744 · UniProt Q9D1J1
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