Research workbench
Open conformation of francisella tularensis clpp at 1.9 a
Analyse Open conformation of francisella tularensis clpp at 1.9 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G1R
- Type
- protein
- Length
- 1,326 residues
- Chains
- 7
- 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
- Q5NH47
- Pockets
- 20 · best druggability 0.64
Structure
x-ray diffraction · 7 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 193 | 44% helix, 23% strand | Q5NH47 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 46% helix, 21% strand | Q5NH47 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 190 | 45% helix, 21% strand | Q5NH47 |
| D | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 45% helix, 21% strand | Q5NH47 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 189 | 44% helix, 22% strand | Q5NH47 |
| F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 43% helix, 24% strand | Q5NH47 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 194 | 44% helix, 20% strand | Q5NH47 |
Ligands and binding sites
- ACT · Acetate ion · additive · 7 copies · chains A, B, C, D, F, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B, E, F, G
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.64 | 0.74 | 81 | empty |
| 2 | 223 | 0.64 | 0.82 | 27 | empty |
| 3 | 264 | 0.62 | 0.80 | 39 | ACT |
| 4 | 265 | 0.60 | 0.79 | 41 | ACT |
| 5 | 244 | 0.59 | 0.79 | 39 | empty |
Interfaces
12 interfaces between chains.
- F–G · 2155 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1896 Ų buried · 26 hydrogen bonds · protein-protein
- A–G · 1853 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 1783 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1746 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5G1R · Open conformation of Francisella tularensis ClpP at 1.9 A · the same entry in another collection · chain G against G, TM-score 1.00
- Q5NH47 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease proteolytic subunit… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q5NH47
- Elsewhere: RCSB PDB 5G1R · PDBe 5G1R · UniProt Q5NH47
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