Research workbench
Legionella pneumophila NTPDASE1 crystal form III (closed) in complex with mg AMP
Analyse Legionella pneumophila NTPDASE1 crystal form III (closed) in complex with mg AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BRN
- Type
- protein
- Length
- 714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleoside triphosphate diphosphohydrolase I
- UniProt
- Q5ZUA2
- Ligands
- AMP, MG, CL
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleoside triphosphate diphosphohydrolase I | protein | 356 | 41% helix, 25% strand | Q5ZUA2 |
| B | Ectonucleoside triphosphate diphosphohydrolase I | protein | 358 | 41% helix, 25% strand | Q5ZUA2 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.85 | 0.86 | 101 | AMP, MG |
| 2 | 374 | 0.72 | 0.84 | 48 | AMP, MG |
| 3 | 186 | 0.56 | 0.80 | 26 | CL |
| 4 | 210 | 0.54 | 0.78 | 31 | CL |
| 5 | 89 | 0.48 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1516 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4BRN · Legionella pneumophila NTPDase1 crystal form III (closed) in complex with Mg AMP · 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 4BRN · PDBe 4BRN · UniProt Q5ZUA2
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