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Complex between the salmonella T3SS effector slrp and its human target thioredoxin-1
Analyse Complex between the salmonella T3SS effector slrp and its human target… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PUF
- Type
- protein
- Length
- 1,421 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase slrp; Thioredoxin
- EC
- 6.3.2.-
- UniProt
- D0ZRB2, P10599
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase slrp (EC 6.3.2.-) | protein | 599 | 39% helix, 8% strand | D0ZRB2 |
| B | E3 ubiquitin-protein ligase slrp (EC 6.3.2.-) | protein | 598 | 37% helix, 9% strand | D0ZRB2 |
| C, D | Thioredoxin | protein | 112 | 32% helix, 21% strand | P10599 |
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.80 | 0.95 | 44 | empty |
| 2 | 935 | 0.79 | 0.81 | 111 | empty |
| 3 | 118 | 0.78 | 0.96 | 26 | empty |
| 4 | 83 | 0.77 | 0.98 | 20 | empty |
| 5 | 804 | 0.76 | 0.80 | 73 | empty |
Interfaces
6 interfaces between chains.
- B–C · 866 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 791 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 712 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 681 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 135 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4PUF · Complex between the Salmonella T3SS effector SlrP and its human target thioredoxin-1 · the same entry in another collection · chain A against A, TM-score 1.00
- D0ZRB2 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase slrp (D0ZRB2) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P10599 · AlphaFold monomer V2.0 prediction for thioredoxin (P10599) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 D0ZRB2
- Every structure of UniProt P10599
- Elsewhere: RCSB PDB 4PUF · PDBe 4PUF · UniProt D0ZRB2 · UniProt P10599
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