MolNFT v1 · #163875 · protein
Cryo-EM structure of CLPP1/2 in the LMCLPXP1/2 complex
6SFX · ATP-dependent clp protease proteolytic subunit: “Cryo-EM structure of CLPP1/2 in the LMCLPXP1/2 complex”. Electron microscopy, 20 pockets (best druggability 0.76). MolNFT v1 #163875 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6SFX
- Type
- protein
- Length
- 2,602 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit
- EC
- 3.4.21.92
- UniProt
- A0A3T2ER33, A0A0B8R1W1
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 7 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 51% helix, 17% strand | A0A3T2ER33 |
| H | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 193 | 43% helix, 21% strand | A0A0B8R1W1 |
| I | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 198 | 42% helix, 16% strand | A0A0B8R1W1 |
| J | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 41% helix, 20% strand | A0A0B8R1W1 |
| K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 190 | 47% helix, 15% strand | A0A0B8R1W1 |
| L, M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 194 | 42% helix, 20% strand | A0A0B8R1W1 |
| N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 195 | 43% helix, 18% strand | A0A0B8R1W1 |
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 | 490 | 0.76 | 0.84 | 62 | empty |
| 2 | 189 | 0.68 | 0.87 | 44 | empty |
| 3 | 457 | 0.67 | 0.79 | 46 | empty |
| 4 | 707 | 0.67 | 0.75 | 99 | empty |
| 5 | 163 | 0.65 | 0.86 | 27 | empty |
Interfaces
39 interfaces between chains.
- I–J · 1907 Ų buried · 18 hydrogen bonds · protein-protein
- M–N · 1841 Ų buried · 22 hydrogen bonds · protein-protein
- H–N · 1834 Ų buried · 20 hydrogen bonds · protein-protein
- H–I · 1782 Ų buried · 24 hydrogen bonds · protein-protein
- L–M · 1782 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 6SFX · Cryo-EM structure of ClpP1/2 in the LmClpXP1/2 complex · 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 A0A3T2ER33
- Every structure of UniProt A0A0B8R1W1
- Elsewhere: RCSB PDB 6SFX · PDBe 6SFX · UniProt A0A3T2ER33 · UniProt A0A0B8R1W1
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