MolNFT v1 · #178398 · protein
Cryo-EM structure of bsclpp-ADEP1 complex at pH 6.5
7FEP · ATP-dependent clp protease proteolytic subunit: “Cryo-EM structure of bsclpp-ADEP1 complex at pH 6.5”. Electron microscopy, 1 ligand (OTT), 20 pockets (best druggability 0.71). MolNFT v1 #178398 on GenesisL1: 3D structure, binding…
- PDB
- 7FEP
- Type
- protein
- Length
- 2,730 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit; ADEP1
- EC
- 3.4.21.92
- UniProt
- P80244
- Ligands
- OTT
- Pockets
- 20 · best druggability 0.71
Structure
electron microscopy · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, I, J, K, L, M, N, H | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 189 | 42% helix, 22% strand | P80244 |
| O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b | ADEP1 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- OTT · (2E,4E,6E)-octa-2,4,6-trienoic acid · ligand · 14 copies · chains B, C, O, D, P, E, Q, F, R, G, S, N, H, T, I, U, J, V, K, W, L, X, M, Y, A, Z, a, b
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 | 285 | 0.71 | 0.85 | 39 | empty |
| 2 | 307 | 0.70 | 0.83 | 38 | empty |
| 3 | 383 | 0.67 | 0.80 | 67 | empty |
| 4 | 348 | 0.66 | 0.81 | 66 | empty |
| 5 | 319 | 0.66 | 0.81 | 52 | empty |
Interfaces
61 interfaces between chains.
- I–J · 1290 Ų buried · 5 hydrogen bonds · protein-protein
- I–H · 1272 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1265 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 1265 Ų buried · 5 hydrogen bonds · protein-protein
- M–N · 1264 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified, 14 covalent (nonstandard, covalent ligand).
Compared structures
- 7FEP · Cryo-EM structure of BsClpP-ADEP1 complex at pH 6.5 · the same entry in another collection · chain L against L, 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 7FEP · PDBe 7FEP · UniProt P80244
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