MolNFT v1 · #184827 · protein
Homology model of the full-length ap-3 complex in an intermediate open conformation
7P3Y · Ap-3 complex subunit delta: “Homology model of the full-length ap-3 complex in an intermediate open conformation”. Electron microscopy, 18 pockets (best druggability 0.84). MolNFT v1 #184827 on GenesisL1: 3D structure, binding sites…
- PDB
- 7P3Y
- Type
- protein
- Length
- 1,762 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ap-3 complex subunit delta; Y55_G0035830.MRNA.1.CDS.1; Ap-3 complex subunit mu; Ap…
- UniProt
- A0A7I9C4X2, A0A7I9BYB9, P38153, A0A6L1B7P9
- Pockets
- 18 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ap-3 complex subunit delta | protein | 576 | 74% helix, 0% strand | A0A7I9C4X2 |
| B | Y55_G0035830.MRNA.1.CDS.1 | protein | 621 | 75% helix, 0% strand | A0A7I9BYB9 |
| M | Ap-3 complex subunit mu | protein | 397 | 12% helix, 39% strand | P38153 |
| S | Ap complex subunit sigma | protein | 168 | 44% helix, 19% strand | A0A6L1B7P9 |
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.84 | 0.85 | 138 | empty |
| 2 | 649 | 0.77 | 0.83 | 85 | empty |
| 3 | 742 | 0.73 | 0.79 | 78 | empty |
| 4 | 484 | 0.70 | 0.80 | 61 | empty |
| 5 | 493 | 0.70 | 0.80 | 47 | empty |
Interfaces
5 interfaces between chains.
- B–M · 2473 Ų buried · 68 hydrogen bonds · protein-protein
- A–S · 2370 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 1383 Ų buried · 61 hydrogen bonds · protein-protein
- A–M · 219 Ų buried · 9 hydrogen bonds · protein-protein
- B–S · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 isopeptide (isopeptide).
Compared structures
- 7P3Y · Homology model of the full-length AP-3 complex in an intermediate open conformation · the same entry in another collection · chain A against A, TM-score 1.00
- P38153 · AlphaFold monomer V2.0 prediction for ap-3 complex subunit mu (P38153) · a predicted model of the same protein · chain M against A, TM-score 0.78
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 A0A7I9C4X2
- Every structure of UniProt A0A7I9BYB9
- Every structure of UniProt P38153
- Every structure of UniProt A0A6L1B7P9
- Elsewhere: RCSB PDB 7P3Y · PDBe 7P3Y · UniProt A0A7I9C4X2 · UniProt A0A7I9BYB9 · UniProt P38153 · UniProt A0A6L1B7P9
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