Research workbench
Homology model of the full-length ap-3 complex in a stretched open conformation
Analyse Homology model of the full-length ap-3 complex in a stretched open conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P3Z
- Type
- protein
- Length
- 1,756 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
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 55% helix, 8% 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 | 69% helix, 0% strand | A0A7I9BYB9 |
| M | Ap-3 complex subunit mu | protein | 391 | 12% helix, 29% strand | P38153 |
| S | Ap complex subunit sigma | protein | 168 | 43% helix, 17% strand | A0A6L1B7P9 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.84 | 0.88 | 100 | empty |
| 2 | 489 | 0.76 | 0.84 | 57 | empty |
| 3 | 88 | 0.70 | 0.93 | 23 | empty |
| 4 | 379 | 0.70 | 0.82 | 46 | empty |
| 5 | 725 | 0.68 | 0.75 | 58 | empty |
Interfaces
4 interfaces between chains.
- A–S · 2469 Ų buried · 104 hydrogen bonds · protein-protein
- B–M · 2000 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1697 Ų buried · 84 hydrogen bonds · protein-protein
- A–M · 147 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 isopeptide (isopeptide).
Compared structures
- 7P3Z · Homology model of the full-length AP-3 complex in a stretched 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 0.71
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 7P3Z · PDBe 7P3Z · UniProt A0A7I9C4X2 · UniProt A0A7I9BYB9 · UniProt P38153 · UniProt A0A6L1B7P9
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