MolNFT v1 · #167991 · protein
Clpa ENGAGED1 state bound to repa-GFP (clpa focused refinement)
6W22 · ATP-dependent clp protease ATP-binding subunit clpa: “Clpa ENGAGED1 state bound to repa-GFP (clpa focused refinement)”. Electron microscopy, 2 ligands (ATP, ADP), 20 pockets (best druggability 0.87). MolNFT v1 #167991 on GenesisL1…
- PDB
- 6W22
- Type
- protein
- Length
- 3,492 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 0.87
Structure
electron microscopy · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | ATP-dependent clp protease ATP-binding subunit clpa | protein | 578 | 47% helix, 15% strand | P0ABH9 |
| X | Repa, green fluorescent protein fusion | protein | 24 | 0% helix, 13% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, F, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, E, F
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 | 1043 | 0.87 | 0.89 | 143 | empty |
| 2 | 746 | 0.85 | 0.88 | 86 | ATP |
| 3 | 909 | 0.85 | 0.86 | 86 | empty |
| 4 | 873 | 0.84 | 0.87 | 98 | ATP |
| 5 | 611 | 0.84 | 0.89 | 75 | empty |
Interfaces
14 interfaces between chains.
- B–C · 4247 Ų buried · 66 hydrogen bonds · protein-protein
- C–D · 4153 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 3860 Ų buried · 58 hydrogen bonds · protein-protein
- D–E · 3273 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2055 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6W22 · ClpA Engaged1 State bound to RepA-GFP (ClpA Focused Refinement) · 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 0.89
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 6W22 · PDBe 6W22 · UniProt P0ABH9
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