Research workbench
Versatile modes of peptide recognition by the aaa+ adaptor protein sspb- the crystal structure of a sspb-rsea complex
Analyse Versatile modes of peptide recognition by the aaa+ adaptor protein sspb- the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YFN
- Type
- protein
- Length
- 493 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stringent starvation protein B; Sigma-E factor negative regulatory protein
- UniProt
- P0AFZ3, P38106
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stringent starvation protein B | protein | 109 | 21% helix, 39% strand | P0AFZ3 |
| B, C, D | Stringent starvation protein B | protein | 107 | 21% helix, 40% strand | P0AFZ3 |
| E | Sigma-E factor negative regulatory protein | protein | 18 | 50% helix, 0% strand | P38106 |
| F, G, H | Sigma-E factor negative regulatory protein | protein | 15 | 27% helix, 0% strand | P38106 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.59 | 0.77 | 33 | empty |
| 2 | 107 | 0.41 | 0.76 | 17 | empty |
| 3 | 100 | 0.40 | 0.76 | 17 | empty |
| 4 | 62 | 0.35 | 0.78 | 22 | empty |
Interfaces
8 interfaces between chains.
- A–E · 879 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 790 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 785 Ų buried · 7 hydrogen bonds · protein-protein
- C–G · 780 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 760 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1YFN · Versatile modes of peptide recognition by the AAA+ adaptor protein SspB- the crystal… · the same entry in another collection · chain C against C, TM-score 1.00
- P0AFZ3 · AlphaFold monomer V2.0 prediction for stringent starvation protein B (P0AFZ3) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P0AFZ3
- Every structure of UniProt P38106
- Elsewhere: RCSB PDB 1YFN · PDBe 1YFN · UniProt P0AFZ3 · UniProt P38106
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