Research workbench
X-ray structure of the E89A variant of ankyrin repeat domain of DHHC17 in complex with SNAP25B peptide
Analyse X-ray structure of the E89A variant of ankyrin repeat domain of DHHC17 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W7J
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Palmitoyltransferase ZDHHC17; SNAP25B-111-120
- EC
- 2.3.1.225
- UniProt
- Q8IUH5
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Palmitoyltransferase ZDHHC17 (EC 2.3.1.225) | protein | 229 | 48% helix, 3% strand | Q8IUH5 |
| B, D | SNAP25B-111-120 | protein | 10 | 0% helix, 0% strand | — |
| C | Palmitoyltransferase ZDHHC17 (EC 2.3.1.225) | protein | 231 | 48% helix, 3% strand | Q8IUH5 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.69 | 0.79 | 64 | empty |
| 2 | 306 | 0.60 | 0.78 | 35 | empty |
| 3 | 88 | 0.42 | 0.79 | 14 | empty |
| 4 | 74 | 0.41 | 0.80 | 15 | empty |
| 5 | 131 | 0.39 | 0.74 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–C · 972 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 524 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 518 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 191 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 183 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5W7J · X-ray structure of the E89A variant of ankyrin repeat domain of DHHC17 in complex with… · the same entry in another collection · chain C against C, TM-score 1.00
- Q8IUH5 · AlphaFold monomer V2.0 prediction for palmitoyltransferase ZDHHC17 (Q8IUH5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8IUH5
- Elsewhere: RCSB PDB 5W7J · PDBe 5W7J · UniProt Q8IUH5
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