Research workbench
AP2 bound to heparin in the closed conformation
Analyse AP2 bound to heparin in the closed conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RW8
- Type
- protein
- Length
- 1,712 residues
- Chains
- 4
- 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
- P17427, Q9DBG3, P84091, P62743
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ap-2 complex subunit alpha-2 | protein | 598 | 73% helix, 0% strand | P17427 |
| B | Ap-2 complex subunit beta | protein | 579 | 65% helix, 0% strand | Q9DBG3 |
| M | Ap-2 complex subunit mu | protein | 394 | 13% helix, 46% strand | P84091 |
| S | Ap-2 complex subunit sigma | protein | 141 | 46% helix, 26% strand | P62743 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.81 | 0.82 | 87 | empty |
| 2 | 890 | 0.80 | 0.82 | 112 | empty |
| 3 | 1041 | 0.74 | 0.77 | 98 | empty |
| 4 | 579 | 0.74 | 0.81 | 58 | empty |
| 5 | 478 | 0.72 | 0.81 | 49 | empty |
Interfaces
6 interfaces between chains.
- B–M · 2771 Ų buried · 14 hydrogen bonds · protein-protein
- A–S · 2224 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1439 Ų buried · 12 hydrogen bonds · protein-protein
- A–M · 810 Ų buried · 4 hydrogen bonds · protein-protein
- B–S · 465 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7RW8 · AP2 bound to heparin in the closed 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
- 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 0.92
- P17427 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit alpha-2 (P17427) · a predicted model of the same protein · chain A against A, TM-score 0.84
- 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 P17427
- Every structure of UniProt Q9DBG3
- Every structure of UniProt P84091
- Every structure of UniProt P62743
- Elsewhere: RCSB PDB 7RW8 · PDBe 7RW8 · UniProt P17427 · UniProt Q9DBG3 · UniProt P84091 · UniProt P62743
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