Research workbench
The structure of the caulobacter crescentus clps protease adaptor protein in complex with a N-end rule peptide
Analyse The structure of the caulobacter crescentus clps protease adaptor protein in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DNJ
- Type
- protein
- Length
- 167 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease adapter protein clps; Synthetic N-end rule peptide
- UniProt
- Q9A5I0
- Ligands
- MG
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease adapter protein clps | protein | 80 | 54% helix, 24% strand | Q9A5I0 |
| B | ATP-dependent clp protease adapter protein clps | protein | 81 | 52% helix, 26% strand | Q9A5I0 |
| C, D | Synthetic N-end rule peptide | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.36 | 0.73 | 21 | empty |
| 2 | 56 | 0.26 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 485 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 306 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 295 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3DNJ · The structure of the Caulobacter crescentus ClpS protease adaptor protein in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9A5I0 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease adapter protein clps… · a predicted model of the same protein · chain A 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 Q9A5I0
- Elsewhere: RCSB PDB 3DNJ · PDBe 3DNJ · UniProt Q9A5I0
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