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Crystal structure of clpp from bacillus subtilis in complex with ADEP2 (compact state)
Analyse Crystal structure of clpp from bacillus subtilis in complex with ADEP2 (compact… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P81
- Type
- protein
- Length
- 4,924 residues
- Chains
- 48
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit; ADEP2
- EC
- 3.4.21.92
- UniProt
- P80244
- Ligands
- CXP
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 27 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 172 | 44% helix, 21% strand | P80244 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 176 | 45% helix, 23% strand | P80244 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 172 | 44% helix, 21% strand | P80244 |
| D | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 164 | 46% helix, 17% strand | P80244 |
| E, S | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 174 | 44% helix, 22% strand | P80244 |
| F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 169 | 44% helix, 20% strand | P80244 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 177 | 44% helix, 23% strand | P80244 |
| H | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 172 | 42% helix, 20% strand | P80244 |
| I | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 177 | 44% helix, 21% strand | P80244 |
| J | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 173 | 43% helix, 23% strand | P80244 |
| K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 171 | 46% helix, 18% strand | P80244 |
| L | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 171 | 42% helix, 21% strand | P80244 |
| M, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 168 | 44% helix, 20% strand | P80244 |
| O | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 174 | 44% helix, 20% strand | P80244 |
| P | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 177 | 45% helix, 22% strand | P80244 |
| Q | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 172 | 44% helix, 24% strand | P80244 |
| R | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 168 | 45% helix, 20% strand | P80244 |
| T | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 168 | 43% helix, 21% strand | P80244 |
| U | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 170 | 45% helix, 21% strand | P80244 |
| V | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 175 | 45% helix, 21% strand | P80244 |
| W | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 176 | 44% helix, 21% strand | P80244 |
| X | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 169 | 44% helix, 20% strand | P80244 |
| Y | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 165 | 45% helix, 17% strand | P80244 |
| Z | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 169 | 43% helix, 20% strand | P80244 |
| a | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 168 | 45% helix, 22% strand | P80244 |
| b | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 175 | 44% helix, 24% strand | P80244 |
| c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, t, u, v, w | ADEP2 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- CXP · Cyclohexane propionic acid · ligand · 20 copies · chains A, B, c, C, d, D, E, e, F, f, G, g, H, I, h, J, i, K, L, j, M, k, N, l, O, P, m, Q, n, R, S, o, T, p, U, q, V, W, r, X, t, Y, Z, u, a, v, b, w
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 | 800 | 0.71 | 0.77 | 103 | empty |
| 2 | 516 | 0.66 | 0.78 | 56 | empty |
| 3 | 364 | 0.66 | 0.80 | 44 | empty |
| 4 | 330 | 0.65 | 0.80 | 44 | empty |
| 5 | 270 | 0.62 | 0.80 | 38 | empty |
Interfaces
102 interfaces between chains.
- V–W · 1467 Ų buried · 15 hydrogen bonds · protein-protein
- O–P · 1415 Ų buried · 16 hydrogen bonds · protein-protein
- H–I · 1404 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1343 Ų buried · 13 hydrogen bonds · protein-protein
- A–G · 1339 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified, 20 covalent (nonstandard, covalent ligand).
Compared structures
- 7P81 · Crystal structure of ClpP from Bacillus subtilis in complex with ADEP2 (compact state) · the same entry in another collection · chain J against J, 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 7P81 · PDBe 7P81 · UniProt P80244
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