MolNFT v1 · #69539 · protein
Structure of clpp in complex with ADEP1
3KTI · ATP-dependent clp protease proteolytic subunit: “Structure of clpp in complex with ADEP1”. X-ray diffraction, 1 ligand (OTT), 20 pockets (best druggability 0.58). MolNFT v1 #69539 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3KTI
- Type
- protein
- Length
- 1,260 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit; Acyldepsipeptide 1
- EC
- 3.4.21.92
- UniProt
- P80244
- Ligands
- OTT
- Pockets
- 20 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 20% 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 | 174 | 48% helix, 21% strand | P80244 |
| H, I, J, K, L, M, N | Acyldepsipeptide 1 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- OTT · (2E,4E,6E)-octa-2,4,6-trienoic acid · ligand · 7 copies · chains A, B, H, G, I, E, F, J, C, K, D, L, M, N
- DMS · Dimethyl sulfoxide · additive · 7 copies · chains A, B, C, D, E, F, G
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 7 copies · chains A, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.58 | 0.91 | 20 | DMS |
| 2 | 50 | 0.58 | 0.91 | 17 | DMS |
| 3 | 52 | 0.58 | 0.91 | 17 | DMS |
| 4 | 51 | 0.57 | 0.90 | 18 | DMS |
| 5 | 55 | 0.55 | 0.89 | 17 | DMS |
Interfaces
21 interfaces between chains.
- B–C · 1044 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1032 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1028 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1024 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1015 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 7 covalent (nonstandard, covalent ligand).
Compared structures
- 3KTI · Structure of ClpP in complex with ADEP1 · 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 P80244
- Elsewhere: RCSB PDB 3KTI · PDBe 3KTI · UniProt P80244
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