Research workbench
ATP-dependent clp protease ATP-binding subunit CLPA/ATP-dependent clp protease adaptor protein clps
Analyse ATP-dependent clp protease ATP-binding subunit CLPA/ATP-dependent clp protease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R6O
- Type
- protein
- Length
- 471 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease ATP-binding subunit clpa; ATP-dependent clp protease adaptor…
- UniProt
- P0ABH9, P0A8Q6
- Ligands
- YBT, ZN, Y1, CL
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease ATP-binding subunit clpa | protein | 142 | 63% helix, 6% strand | P0ABH9 |
| B | ATP-dependent clp protease ATP-binding subunit clpa | protein | 141 | 64% helix, 6% strand | P0ABH9 |
| C | ATP-dependent clp protease adaptor protein clps | protein | 94 | 46% helix, 22% strand | P0A8Q6 |
| D | ATP-dependent clp protease adaptor protein clps | protein | 94 | 46% helix, 22% strand | P0A8Q6 |
Ligands and binding sites
- YBT · Bis-(2-hydroxyethyl)amino-tris(hydroxymethyl)methane yttrium · ligand · 4 copies · chains A, C, D, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- Y1 · Yttrium ion · metal · 2 copies · chains A, D
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.41 | 0.81 | 13 | Y1 |
| 2 | 108 | 0.38 | 0.75 | 18 | empty |
| 3 | 58 | 0.28 | 0.74 | 14 | empty |
| 4 | 50 | 0.25 | 0.73 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1321 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1277 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 491 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 146 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1R6O · ATP-dependent Clp protease ATP-binding subunit clpA/ATP-dependent Clp protease adaptor… · the same entry in another collection · chain D against D, TM-score 1.00
- P0ABH9 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease ATP- binding subunit… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P0A8Q6 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease adapter protein clps… · a predicted model of the same protein · chain C against A, TM-score 0.88
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 P0ABH9
- Every structure of UniProt P0A8Q6
- Elsewhere: RCSB PDB 1R6O · PDBe 1R6O · UniProt P0ABH9 · UniProt P0A8Q6
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