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Helical structure of membrane tubules decorated by ACAP1 (barph doamin) protein by cryo-electron microscopy and md simulation
Analyse Helical structure of membrane tubules decorated by ACAP1 (barph doamin) protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H3D
- Type
- protein
- Length
- 1,450 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arf-gap with coiled-coil, ank repeat and pH domain- containing protein 1
- UniProt
- Q15027
- Pockets
- 9 · best druggability 0.77
Structure
electron microscopy · 2 distinct chains · 67% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Arf-gap with coiled-coil, ank repeat and pH domain- containing protein 1 | protein | 364 | 67% helix, 11% strand | Q15027 |
| B, D | Arf-gap with coiled-coil, ank repeat and pH domain- containing protein 1 | protein | 361 | 67% helix, 12% strand | Q15027 |
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.77 | 0.80 | 67 | empty |
| 2 | 79 | 0.76 | 0.98 | 20 | empty |
| 3 | 73 | 0.74 | 0.98 | 19 | empty |
| 4 | 54 | 0.72 | 0.98 | 18 | empty |
| 5 | 201 | 0.64 | 0.84 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–B · 6296 Ų buried · 79 hydrogen bonds · protein-protein
- C–D · 6227 Ų buried · 91 hydrogen bonds · protein-protein
- A–C · 496 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 289 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5H3D · Helical structure of membrane tubules decorated by ACAP1 (BARPH doamin) protein by… · the same entry in another collection · chain D against D, TM-score 1.00
- Q15027 · AlphaFold monomer V2.0 prediction for arf-gap with coiled-coil, ank repeat and pH… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q15027
- Elsewhere: RCSB PDB 5H3D · PDBe 5H3D · UniProt Q15027
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