Research workbench
Crystal structure of H.pylori ClpP in complex with the peptide NVLGFTQ
Analyse Crystal structure of H.pylori ClpP in complex with the peptide NVLGFTQ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZL2
- Type
- protein
- Length
- 2,463 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Helicobacter pylori; SYNTHETIC CONSTRUCT
- Molecule
- ATP-dependent Clp protease proteolytic subunit; A peptide substrate-NVLGFTQ; A peptide…
- EC
- 3.4.21.92
- UniProt
- P56156
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.5 · 7 distinct chains · 44% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 174 | 47% helix, 26% strand | P56156 |
| B, D, E, F, G, H, I, J, K, L, M, N | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 173 | 46% helix, 25% strand | P56156 |
| O, Q, T, V, W, X | A peptide substrate-NVLGFTQ | protein | 4 | 0% helix, 25% strand | — |
| P | A peptide substrate-NVLGFTQ | protein | 4 | 0% helix, 25% strand | — |
| R | A peptide substrate-NVLGFTQ for Chain R and S | protein | 3 | 0% helix, 33% strand | — |
| S | A peptide substrate-NVLGFTQ for Chain R and S | protein | 4 | 0% helix, 25% strand | — |
| U | A peptide substrate-NVLGFTQ | protein | 4 | 0% helix, 25% strand | — |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.74 | 0.77 | 134 | empty |
| 2 | 609 | 0.67 | 0.76 | 64 | empty |
| 3 | 562 | 0.65 | 0.76 | 75 | empty |
| 4 | 559 | 0.64 | 0.76 | 65 | empty |
| 5 | 521 | 0.63 | 0.75 | 62 | empty |
Interfaces
52 interfaces between chains.
- A–G · 1206 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1203 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1196 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1192 Ų buried · 9 hydrogen bonds · protein-protein
- I–J · 1190 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2ZL2 · Crystal structure of H.PYLORI clpp in complex with the peptide nvlgftq · 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 P56156
- Elsewhere: RCSB PDB 2ZL2 · PDBe 2ZL2 · UniProt P56156
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