MolNFT v1 · #106415 · protein
CLPP1/2 heterocomplex from listeria monocytogenes
4RYF · ATP-dependent clp protease proteolytic subunit: “CLPP1/2 heterocomplex from listeria monocytogenes”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.67). MolNFT v1 #106415 on GenesisL1: 3D structure, binding sites…
- PDB
- 4RYF
- Type
- protein
- Length
- 2,533 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
- Q8Y7Y1, Q9RQI6
- Ligands
- NA
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 49% helix, 27% strand | Q8Y7Y1 |
| B, C, E, F, G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 49% helix, 27% strand | Q8Y7Y1 |
| H, I, M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 45% helix, 25% strand | Q9RQI6 |
| J, K, L, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 45% helix, 24% strand | Q9RQI6 |
Ligands and binding sites
- NA · Sodium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- MLI · Malonate ion · additive · 7 copies · chains H, I, J, K, L, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.67 | 0.93 | 20 | MLI |
| 2 | 86 | 0.67 | 0.92 | 18 | MLI |
| 3 | 78 | 0.67 | 0.92 | 18 | MLI |
| 4 | 77 | 0.66 | 0.92 | 19 | MLI |
| 5 | 81 | 0.65 | 0.91 | 20 | MLI |
Interfaces
38 interfaces between chains.
- I–J · 1651 Ų buried · 14 hydrogen bonds · protein-protein
- L–M · 1640 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 1636 Ų buried · 15 hydrogen bonds · protein-protein
- H–I · 1617 Ų buried · 14 hydrogen bonds · protein-protein
- M–N · 1615 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4RYF · ClpP1/2 heterocomplex from Listeria monocytogenes · the same entry in another collection · chain N against N, 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 Q8Y7Y1
- Every structure of UniProt Q9RQI6
- Elsewhere: RCSB PDB 4RYF · PDBe 4RYF · UniProt Q8Y7Y1 · UniProt Q9RQI6
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