Research workbench
Crystal structure of Helicobacter pylori ATP dependent protease, FtsH ADP complex
Analyse Crystal structure of Helicobacter pylori ATP dependent protease, FtsH ADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R65
- Type
- protein
- Length
- 1,245 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Helicobacter pylori
- Molecule
- Cell division protease ftsH homolog
- EC
- 3.4.24.-
- UniProt
- P71408
- Ligands
- ADP
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · resolution 3.3 · 1 distinct chain · 40% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Cell division protease ftsH homolog (EC 3.4.24.-) | protein | 249 | 40% helix, 10% strand | P71408 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.72 | 0.76 | 96 | ADP |
| 2 | 1192 | 0.71 | 0.75 | 101 | ADP |
| 3 | 453 | 0.71 | 0.81 | 40 | empty |
| 4 | 123 | 0.68 | 0.90 | 25 | empty |
| 5 | 578 | 0.68 | 0.77 | 51 | empty |
Interfaces
4 interfaces between chains.
- D–E · 821 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 778 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 760 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 743 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2R65 · Crystal structure of helicobacter pylori ATP dependent protease, ftsh ADP complex · the same entry in another collection · chain E against E, TM-score 1.00
- P71408 · AlphaFold monomer V2.0 prediction for ATP-dependent zinc metalloprotease ftsh (P71408) · a predicted model of the same protein · chain E against A, TM-score 0.92
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 P71408
- Elsewhere: RCSB PDB 2R65 · PDBe 2R65 · UniProt P71408
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