Research workbench
CLPA/CLPP disengaged state bound to repa-GFP
Analyse CLPA/CLPP disengaged state bound to repa-GFP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UQE
- Type
- protein
- Length
- 6,161 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease ATP-binding subunit clpa; ATP-dependent clp protease…
- EC
- 3.4.21.92
- UniProt
- A0A4Y9BNB2, A0A0K4NM46
- Ligands
- AGS, ADP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease ATP-binding subunit clpa | protein | 562 | 46% helix, 14% strand | A0A4Y9BNB2 |
| B, C, D, E, F | ATP-dependent clp protease ATP-binding subunit clpa | protein | 578 | 41% helix, 14% strand | A0A4Y9BNB2 |
| G, H, I, J, K, L, M, N, O, P, Q, R, S, T | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 41% helix, 24% strand | A0A0K4NM46 |
| X | Repa-GFP | protein | 10 | 0% helix, 0% strand | — |
| Y | Repa-GFP | protein | 11 | 0% helix, 9% strand | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 7 copies · chains B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, F, D, 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 | 844 | 0.86 | 0.88 | 102 | empty |
| 2 | 895 | 0.85 | 0.86 | 110 | AGS |
| 3 | 680 | 0.84 | 0.88 | 93 | AGS |
| 4 | 789 | 0.82 | 0.86 | 75 | AGS |
| 5 | 618 | 0.82 | 0.87 | 58 | AGS |
Interfaces
69 interfaces between chains.
- C–D · 4120 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 4032 Ų buried · 49 hydrogen bonds · protein-protein
- D–E · 3644 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 3313 Ų buried · 46 hydrogen bonds · protein-protein
- E–F · 2094 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6UQE · ClpA/ClpP Disengaged State bound to RepA-GFP · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A4Y9BNB2
- Every structure of UniProt A0A0K4NM46
- Elsewhere: RCSB PDB 6UQE · PDBe 6UQE · UniProt A0A4Y9BNB2 · UniProt A0A0K4NM46
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