Research workbench
The structure of agrobacterium tumefaciens CLPS2 in complex with L- tyrosinamide
Analyse The structure of agrobacterium tumefaciens CLPS2 in complex with L- tyrosinamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YKA
- Type
- protein
- Length
- 333 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease adapter protein clps 2
- UniProt
- Q8UD95
- Ligands
- TYC, SO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | ATP-dependent clp protease adapter protein clps 2 | protein | 83 | 51% helix, 24% strand | Q8UD95 |
| C | ATP-dependent clp protease adapter protein clps 2 | protein | 84 | 51% helix, 25% strand | Q8UD95 |
Ligands and binding sites
- TYC · L-tyrosinamide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.71 | 0.80 | 59 | empty |
| 2 | 57 | 0.55 | 0.89 | 17 | TYC |
| 3 | 66 | 0.32 | 0.76 | 14 | empty |
| 4 | 62 | 0.29 | 0.74 | 14 | empty |
Interfaces
5 interfaces between chains.
- B–D · 623 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 443 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 426 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 249 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 33 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YKA · The structure of Agrobacterium tumefaciens ClpS2 in complex with L-tyrosinamide · the same entry in another collection · chain C against C, TM-score 1.00
- Q8UD95 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease adapter protein clps 2… · a predicted model of the same protein · chain B 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 Q8UD95
- Elsewhere: RCSB PDB 4YKA · PDBe 4YKA · UniProt Q8UD95
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