Research workbench
Structure of the SNX5 px domain in complex with chlamydial protein ince in space group P32
Analyse Structure of the SNX5 px domain in complex with chlamydial protein ince in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TGH
- Type
- protein
- Length
- 652 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sorting nexin-5; Ince
- UniProt
- Q9Y5X3, B7SCI5
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Sorting nexin-5 | protein | 142 | 52% helix, 20% strand | Q9Y5X3 |
| B, D | Ince | protein | 21 | 0% helix, 43% strand | B7SCI5 |
| E, G | Sorting nexin-5 | protein | 143 | 50% helix, 18% strand | Q9Y5X3 |
| F, H | Ince | protein | 20 | 0% helix, 50% strand | B7SCI5 |
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.82 | 0.88 | 58 | empty |
| 2 | 527 | 0.80 | 0.86 | 70 | empty |
| 3 | 150 | 0.66 | 0.87 | 27 | empty |
| 4 | 134 | 0.61 | 0.85 | 20 | empty |
| 5 | 90 | 0.57 | 0.86 | 16 | empty |
Interfaces
16 interfaces between chains.
- C–D · 729 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 707 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 661 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 653 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 652 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5TGH · Structure of the SNX5 PX domain in complex with chlamydial protein IncE in space group P32 · the same entry in another collection · chain H against H, TM-score 1.00
- Q9Y5X3 · AlphaFold monomer V2.0 prediction for sorting nexin-5 (Q9Y5X3) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9Y5X3
- Every structure of UniProt B7SCI5
- Elsewhere: RCSB PDB 5TGH · PDBe 5TGH · UniProt Q9Y5X3 · UniProt B7SCI5
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