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Crystal structure of Neisseria meningitidis ClpP protease E31A+E58A activated double mutant
Analyse Crystal structure of Neisseria meningitidis ClpP protease E31A+E58A activated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NAY
- Type
- protein
- Length
- 4,905 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.199
- Source
- Neisseria meningitidis
- Molecule
- ATP-dependent Clp protease proteolytic subunit
- EC
- 3.4.21.92
- UniProt
- A0A0H5Q9L9
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.199 · 17 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 174 | 48% helix, 22% strand | A0A0H5Q9L9 |
| B, O, a | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 174 | 48% helix, 23% strand | A0A0H5Q9L9 |
| C, L, Q, Z | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 175 | 48% helix, 23% strand | A0A0H5Q9L9 |
| D | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 175 | 48% helix, 22% strand | A0A0H5Q9L9 |
| E | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 173 | 49% helix, 23% strand | A0A0H5Q9L9 |
| F | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 47% helix, 22% strand | A0A0H5Q9L9 |
| G | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 49% helix, 22% strand | A0A0H5Q9L9 |
| H, V | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 175 | 48% helix, 22% strand | A0A0H5Q9L9 |
| I, R, W | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 174 | 48% helix, 22% strand | A0A0H5Q9L9 |
| J, K, T, X | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 176 | 48% helix, 23% strand | A0A0H5Q9L9 |
| M | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 172 | 49% helix, 23% strand | A0A0H5Q9L9 |
| N | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 177 | 47% helix, 23% strand | A0A0H5Q9L9 |
| P | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 177 | 47% helix, 23% strand | A0A0H5Q9L9 |
| S | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 172 | 49% helix, 23% strand | A0A0H5Q9L9 |
| U | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 176 | 48% helix, 23% strand | A0A0H5Q9L9 |
| Y | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 49% helix, 23% strand | A0A0H5Q9L9 |
| b | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 176 | 48% helix, 22% strand | A0A0H5Q9L9 |
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 | 827 | 0.81 | 0.83 | 77 | empty |
| 2 | 1174 | 0.78 | 0.79 | 155 | empty |
| 3 | 964 | 0.76 | 0.79 | 122 | empty |
| 4 | 758 | 0.72 | 0.78 | 102 | empty |
| 5 | 617 | 0.72 | 0.79 | 82 | empty |
Interfaces
75 interfaces between chains.
- O–U · 1341 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1330 Ų buried · 13 hydrogen bonds · protein-protein
- a–b · 1318 Ų buried · 15 hydrogen bonds · protein-protein
- Z–a · 1312 Ų buried · 13 hydrogen bonds · protein-protein
- H–N · 1311 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6NAY · Crystal structure of neisseria meningitidis clpp protease E31A+E58A activated double… · the same entry in another collection · chain B against B, 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 A0A0H5Q9L9
- Elsewhere: RCSB PDB 6NAY · PDBe 6NAY · UniProt A0A0H5Q9L9
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