MolNFT v1 · #157380 · protein
Crystal structure of CLPP1 from clostridium difficile 630.
6MX2 · ATP-dependent clp protease proteolytic subunit: “Crystal structure of CLPP1 from clostridium difficile 630.”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.66). MolNFT v1 #157380 on GenesisL1: 3D structure…
- PDB
- 6MX2
- Type
- protein
- Length
- 2,551 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit
- EC
- 3.4.21.92
- UniProt
- Q180F0
- Ligands
- NA
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 12 distinct chains · 46% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 24% strand | Q180F0 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 185 | 45% helix, 25% strand | Q180F0 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 46% helix, 23% strand | Q180F0 |
| D | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 46% helix, 25% strand | Q180F0 |
| E, K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 47% helix, 24% strand | Q180F0 |
| F, G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 45% helix, 23% strand | Q180F0 |
| H | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 46% helix, 24% strand | Q180F0 |
| I | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 46% helix, 24% strand | Q180F0 |
| J | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 187 | 44% helix, 26% strand | Q180F0 |
| L | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 23% strand | Q180F0 |
| M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 45% helix, 24% strand | Q180F0 |
| N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 47% helix, 23% strand | Q180F0 |
Ligands and binding sites
- NA · Sodium ion · metal · 17 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- GOL · Glycerol · additive · 2 copies · chains M, N
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 | 209 | 0.66 | 0.84 | 29 | empty |
| 2 | 186 | 0.65 | 0.85 | 28 | empty |
| 3 | 191 | 0.64 | 0.84 | 26 | empty |
| 4 | 84 | 0.64 | 0.90 | 18 | empty |
| 5 | 73 | 0.63 | 0.91 | 18 | GOL |
Interfaces
35 interfaces between chains.
- E–F · 1584 Ų buried · 20 hydrogen bonds · protein-protein
- K–L · 1571 Ų buried · 19 hydrogen bonds · protein-protein
- J–K · 1548 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 1538 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1520 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6MX2 · Crystal Structure of ClpP1 from Clostridium difficile 630. · 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 Q180F0
- Elsewhere: RCSB PDB 6MX2 · PDBe 6MX2 · UniProt Q180F0
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