Research workbench
Crystal structure of the SNX27 PDZ domain bound to the C-terminal dgkzeta PDZ binding motif
Analyse Crystal structure of the SNX27 PDZ domain bound to the C-terminal dgkzeta PDZ… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ELQ
- Type
- protein
- Length
- 203 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sorting nexin-27; Glu-asp-gln-glu-thr-ala-val
- UniProt
- Q8K4V4
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sorting nexin-27 | protein | 94 | 14% helix, 41% strand | Q8K4V4 |
| P, C | Glu-asp-gln-glu-thr-ala-val | protein | 7 | 0% helix, 71% strand | — |
| B | Sorting nexin-27 | protein | 95 | 14% helix, 42% strand | Q8K4V4 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.64 | 0.84 | 29 | PG4 |
| 2 | 83 | 0.35 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–P · 526 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 525 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 362 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ELQ · Crystal structure of the SNX27 PDZ domain bound to the C-terminal DGKzeta PDZ binding… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8K4V4 · AlphaFold monomer V2.0 prediction for sorting nexin-27 (Q8K4V4) · 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 Q8K4V4
- Elsewhere: RCSB PDB 5ELQ · PDBe 5ELQ · UniProt Q8K4V4
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