Research workbench
Legionella pneumophila NTPDase1 crystal form III (closed) in complex with transition state mimic guanosine 5'-phosphovanadate
Analyse Legionella pneumophila NTPDase1 crystal form III (closed) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BRL
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- LEGIONELLA PNEUMOPHILA
- Molecule
- Ectonucleoside triphosphate diphosphohydrolase I
- EC
- 3.6.1.5
- UniProt
- Q5ZUA2
- Ligands
- GMV, MG, CL
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.6 · 2 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleoside triphosphate diphosphohydrolase I (EC 3.6.1.5) | protein | 359 | 40% helix, 25% strand | Q5ZUA2 |
| B | Ectonucleoside triphosphate diphosphohydrolase I (EC 3.6.1.5) | protein | 358 | 41% helix, 25% strand | Q5ZUA2 |
Ligands and binding sites
- GMV · Guanosine-5'-phosphovanadate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.79 | 0.86 | 56 | empty |
| 2 | 260 | 0.76 | 0.89 | 42 | GMV, MG |
| 3 | 228 | 0.72 | 0.88 | 37 | GMV, MG |
| 4 | 226 | 0.55 | 0.78 | 26 | CL |
| 5 | 185 | 0.52 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1517 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4BRL · Legionella pneumophila NTPDASE1 crystal form III (closed) in complex with transition… · the same entry in another collection · chain A against A, 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 Q5ZUA2
- Elsewhere: RCSB PDB 4BRL · PDBe 4BRL · UniProt Q5ZUA2
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