Research workbench
Clpap ENGAGED2 state bound to repa-GFP
Analyse Clpap ENGAGED2 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
- 6W21
- Type
- protein
- Length
- 6,147 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease ATP-binding subunit clpa; Repa, green fluorescent protein…
- EC
- 3.4.21.92
- UniProt
- P0ABH9, S1IIE7
- Ligands
- ATP, ADP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 48% helix, 15% 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 | — |
| 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 | 44% helix, 26% strand | S1IIE7 |
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 | 956 | 0.87 | 0.89 | 124 | empty |
| 2 | 1021 | 0.84 | 0.86 | 97 | empty |
| 3 | 758 | 0.83 | 0.86 | 77 | ATP |
| 4 | 659 | 0.82 | 0.87 | 78 | ATP |
| 5 | 1011 | 0.82 | 0.83 | 99 | ADP |
Interfaces
63 interfaces between chains.
- B–C · 4306 Ų buried · 73 hydrogen bonds · protein-protein
- C–D · 4255 Ų buried · 64 hydrogen bonds · protein-protein
- D–E · 3586 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 3504 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 2127 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6W21 · ClpAP Engaged2 State bound to RepA-GFP · the same entry in another collection · chain J against J, 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 P0ABH9
- Every structure of UniProt S1IIE7
- Elsewhere: RCSB PDB 6W21 · PDBe 6W21 · UniProt P0ABH9 · UniProt S1IIE7
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