Research workbench
Clpa ENGAGED2 state bound to repa-GFP (focused classification)
Analyse Clpa ENGAGED2 state bound to repa-GFP (focused classification) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W24
- Type
- protein
- Length
- 3,459 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease ATP-binding subunit clpa; Repa, green fluorescent protein…
- UniProt
- P0ABH9
- Ligands
- ATP, ADP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease ATP-binding subunit clpa | protein | 565 | 47% helix, 14% strand | P0ABH9 |
| B, C, D | ATP-dependent clp protease ATP-binding subunit clpa | protein | 578 | 48% helix, 14% strand | P0ABH9 |
| E, F | ATP-dependent clp protease ATP-binding subunit clpa | protein | 568 | 51% helix, 13% strand | P0ABH9 |
| X | Repa, green fluorescent protein fusion | protein | 24 | 0% helix, 13% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 7 copies · chains A, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, F, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.85 | 0.86 | 115 | ADP |
| 2 | 738 | 0.85 | 0.88 | 104 | empty |
| 3 | 1007 | 0.85 | 0.86 | 95 | empty |
| 4 | 1063 | 0.85 | 0.86 | 117 | ATP |
| 5 | 688 | 0.82 | 0.87 | 82 | ATP |
Interfaces
14 interfaces between chains.
- B–C · 4306 Ų buried · 73 hydrogen bonds · protein-protein
- C–D · 4251 Ų buried · 64 hydrogen bonds · protein-protein
- D–E · 3585 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 3505 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 2127 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6W24 · ClpA Engaged2 State bound to RepA-GFP (Focused Classification) · the same entry in another collection · chain X against X, 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 A 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 P0ABH9
- Elsewhere: RCSB PDB 6W24 · PDBe 6W24 · UniProt P0ABH9
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