MolNFT v1 · #157716 · protein
S. aureus clpp bound to anti-4A
6N80 · ATP-dependent clp protease proteolytic subunit: “S. aureus clpp bound to anti-4A”. X-ray diffraction, 1 ligand (JT7), 20 pockets (best druggability 0.69). MolNFT v1 #157716 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6N80
- Type
- protein
- Length
- 2,524 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
- Q2G036
- Ligands
- JT7
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 11 distinct chains · 46% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, T | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 46% helix, 25% strand | Q2G036 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 177 | 47% helix, 24% strand | Q2G036 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 46% helix, 25% strand | Q2G036 |
| D | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 45% helix, 27% strand | Q2G036 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 25% strand | Q2G036 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 24% strand | Q2G036 |
| I | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 46% helix, 25% strand | Q2G036 |
| K, S | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 47% helix, 24% strand | Q2G036 |
| L | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 46% helix, 27% strand | Q2G036 |
| M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 26% strand | Q2G036 |
| N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 24% strand | Q2G036 |
Ligands and binding sites
- JT7 · N-[(1R)-1-borono-3-methylbutyl]-N~2~-(2-chloro-4-methoxybenzene-1-carbonyl)-L-leucinamide · ligand · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.69 | 0.92 | 20 | JT7 |
| 2 | 423 | 0.67 | 0.80 | 65 | JT7 |
| 3 | 457 | 0.67 | 0.79 | 68 | JT7 |
| 4 | 425 | 0.67 | 0.79 | 65 | JT7 |
| 5 | 96 | 0.67 | 0.91 | 20 | JT7 |
Interfaces
35 interfaces between chains.
- E–F · 1427 Ų buried · 14 hydrogen bonds · protein-protein
- M–N · 1414 Ų buried · 12 hydrogen bonds · protein-protein
- L–M · 1398 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 1370 Ų buried · 9 hydrogen bonds · protein-protein
- N–S · 1359 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 covalent (covalent ligand).
Compared structures
- 6N80 · S. aureus ClpP bound to anti-4a · the same entry in another collection · chain K against K, 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 Q2G036
- Elsewhere: RCSB PDB 6N80 · PDBe 6N80 · UniProt Q2G036
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