MolNFT v1 · #182211 · protein
Crystal structure of escherichia COLI clpp covalently inhibited by clipibicyclene
7MK5 · ATP-dependent clp protease proteolytic subunit: “Crystal structure of escherichia COLI clpp covalently inhibited by clipibicyclene”. X-ray diffraction, 1 ligand (ZGV), 20 pockets (best druggability 0.85). MolNFT v1 #182211 on…
- PDB
- 7MK5
- Type
- protein
- Length
- 5,030 residues
- Chains
- 28
- 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
- P0A6G7
- Ligands
- ZGV
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 17 distinct chains · 47% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 24% strand | P0A6G7 |
| B, D, P | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 46% helix, 25% strand | P0A6G7 |
| C, X | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 25% strand | P0A6G7 |
| F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 47% helix, 24% strand | P0A6G7 |
| G, M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 25% strand | P0A6G7 |
| H | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 177 | 48% helix, 25% strand | P0A6G7 |
| I | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 47% helix, 24% strand | P0A6G7 |
| J, S, V | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 47% helix, 24% strand | P0A6G7 |
| K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 48% helix, 24% strand | P0A6G7 |
| L, T, Y, Z | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 25% strand | P0A6G7 |
| N, b | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 47% helix, 24% strand | P0A6G7 |
| O | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 24% strand | P0A6G7 |
| Q | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 47% helix, 24% strand | P0A6G7 |
| R | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 47% helix, 25% strand | P0A6G7 |
| U | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 24% strand | P0A6G7 |
| W | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 174 | 49% helix, 25% strand | P0A6G7 |
| a | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 177 | 47% helix, 24% strand | P0A6G7 |
Ligands and binding sites
- ZGV · 4-[(1E)-3-{[(2E,4E,6E,8S)-8-hydroxy-4-methyldeca-2,4,6-trienoyl]amino}-3-oxoprop-1-en-1-yl]azete-1(2H)-carboxylic acid · ligand · 28 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, U, P, Q, R, S, T, V, W, X, Y, Z, a, b
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 50 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b
- ACT · Acetate ion · additive · 10 copies · chains A, B, I, P, C, J, F, M, G, E, L, W, R, Y, Q, X, S, Z
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 | 924 | 0.85 | 0.86 | 113 | ACT |
| 2 | 595 | 0.80 | 0.85 | 84 | MPD, ZGV |
| 3 | 900 | 0.79 | 0.82 | 110 | MPD, ZGV |
| 4 | 549 | 0.79 | 0.85 | 76 | MPD |
| 5 | 905 | 0.79 | 0.81 | 114 | MPD |
Interfaces
76 interfaces between chains.
- I–J · 1674 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1669 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1667 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 1661 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1647 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 covalent (covalent ligand).
Compared structures
- 7MK5 · Crystal structure of Escherichia coli ClpP covalently inhibited by clipibicyclene · 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 P0A6G7
- Elsewhere: RCSB PDB 7MK5 · PDBe 7MK5 · UniProt P0A6G7
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