Research workbench
CLPA/CLPP engaged state bound to repa-GFP
Analyse CLPA/CLPP engaged 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
- 6UQO
- Type
- protein
- Length
- 6,174 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 endopeptidase…
- EC
- 3.4.21.92
- UniProt
- A0A4S4P650, A0A4V3YU15
- Ligands
- AGS, ADP
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | ATP-dependent clp protease ATP-binding subunit clpa (EC 3.4.21.92) | protein | 578 | 47% helix, 15% strand | A0A4S4P650 |
| G, H, I, J, K, L, M, N, O, P, Q, R, S, T | ATP-dependent clp endopeptidase proteolytic subunit clpp (EC 3.4.21.92) | protein | 192 | 43% helix, 26% strand | A0A4V3YU15 |
| X, Y | Repa-GFP | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 7 copies · chains A, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, F, 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 | 985 | 0.88 | 0.89 | 132 | empty |
| 2 | 1014 | 0.85 | 0.86 | 112 | AGS |
| 3 | 591 | 0.84 | 0.90 | 89 | empty |
| 4 | 1164 | 0.84 | 0.85 | 114 | AGS |
| 5 | 804 | 0.83 | 0.86 | 84 | empty |
Interfaces
69 interfaces between chains.
- C–D · 3970 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 3952 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 3615 Ų buried · 51 hydrogen bonds · protein-protein
- D–E · 2968 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1959 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 6UQO · ClpA/ClpP Engaged State bound to RepA-GFP · the same entry in another collection · chain C against C, 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 A0A4S4P650
- Every structure of UniProt A0A4V3YU15
- Elsewhere: RCSB PDB 6UQO · PDBe 6UQO · UniProt A0A4S4P650 · UniProt A0A4V3YU15
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