Research workbench
ADEP4 bound to E. faecium clpp
Analyse ADEP4 bound to E. faecium clpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CFD
- Type
- protein
- Length
- 2,548 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
- A0A133CH35
- Ligands
- EZA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 10 distinct chains · 46% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 46% helix, 26% strand | A0A133CH35 |
| B, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 26% strand | A0A133CH35 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 47% helix, 26% strand | A0A133CH35 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 46% helix, 27% strand | A0A133CH35 |
| F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 27% strand | A0A133CH35 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 26% strand | A0A133CH35 |
| I | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 188 | 45% helix, 26% strand | A0A133CH35 |
| K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 27% strand | A0A133CH35 |
| L, S | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 47% helix, 26% strand | A0A133CH35 |
| T | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 46% helix, 27% strand | A0A133CH35 |
Ligands and binding sites
- EZA · N-[(6as,12s,15as,17r,21r,23as)-17,21-dimethyl-6,11,15, 20,23-pentaoxooctadecahydro-2H,6H,11H,15H-pyrido[2,1-i]dipyrrolo[2,1-C:2',1'-L][1,4,7,10, 13]oxatetraazacyclohexadecin-12-yl]-3,5-difluoro-nalpha-[(2E)-hept-2-enoyl]-L-phenylalaninamide · ligand · 11 copies · chains A, B, C, D, E, F, G, I, K, L, M, N, S, T
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 14 copies · chains A, B, C, D, E, F, G, I, K, L, M, N, S, T
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 | 898 | 0.75 | 0.78 | 107 | MPD |
| 2 | 435 | 0.70 | 0.81 | 65 | MPD |
| 3 | 411 | 0.69 | 0.81 | 58 | MPD |
| 4 | 447 | 0.68 | 0.80 | 66 | MPD |
| 5 | 360 | 0.64 | 0.79 | 44 | empty |
Interfaces
35 interfaces between chains.
- A–G · 1380 Ų buried · 13 hydrogen bonds · protein-protein
- I–K · 1340 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1338 Ų buried · 12 hydrogen bonds · protein-protein
- I–T · 1331 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1326 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6CFD · ADEP4 bound to E. faecium ClpP · the same entry in another collection · chain S against S, 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 A0A133CH35
- Elsewhere: RCSB PDB 6CFD · PDBe 6CFD · UniProt A0A133CH35
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