MolNFT v1 · #157792 · protein
Crystal structure of neisseria meningitidis clpp protease in apo form
6NAQ · ATP-dependent clp protease proteolytic subunit: “Crystal structure of neisseria meningitidis clpp protease in apo form”. X-ray diffraction, 1 ligand (K), 20 pockets (best druggability 0.76). MolNFT v1 #157792 on GenesisL1: 3D…
- PDB
- 6NAQ
- Type
- protein
- Length
- 2,578 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
- I4E574
- Ligands
- K
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 10 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 45% helix, 23% strand | I4E574 |
| B, D, F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 45% helix, 22% strand | I4E574 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 22% strand | I4E574 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 45% helix, 22% strand | I4E574 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 187 | 44% helix, 22% strand | I4E574 |
| H | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 187 | 44% helix, 22% strand | I4E574 |
| I | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 185 | 45% helix, 22% strand | I4E574 |
| J | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 47% helix, 22% strand | I4E574 |
| L | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 45% helix, 23% strand | I4E574 |
| M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 45% helix, 22% strand | I4E574 |
Ligands and binding sites
- K · Potassium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
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 | 999 | 0.76 | 0.78 | 100 | empty |
| 2 | 793 | 0.74 | 0.79 | 94 | empty |
| 3 | 820 | 0.74 | 0.79 | 96 | empty |
| 4 | 846 | 0.74 | 0.78 | 95 | empty |
| 5 | 441 | 0.70 | 0.80 | 62 | empty |
Interfaces
35 interfaces between chains.
- D–E · 1581 Ų buried · 21 hydrogen bonds · protein-protein
- I–J · 1580 Ų buried · 20 hydrogen bonds · protein-protein
- A–G · 1576 Ų buried · 21 hydrogen bonds · protein-protein
- F–G · 1571 Ų buried · 20 hydrogen bonds · protein-protein
- K–L · 1569 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6NAQ · Crystal structure of Neisseria meningitidis ClpP protease in Apo form · the same entry in another collection · chain M against M, 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 I4E574
- Elsewhere: RCSB PDB 6NAQ · PDBe 6NAQ · UniProt I4E574
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