Research workbench
Legionella pneumophila NTPDASE1 Q193E crystal form II, closed, mg amppnp complex
Analyse Legionella pneumophila NTPDASE1 Q193E crystal form II, closed, mg amppnp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BRD
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleoside triphosphate diphosphohydrolase I
- EC
- 3.6.1.5
- UniProt
- Q5ZUA2
- Ligands
- ANP, MG, CL
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 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 | 40% helix, 26% strand | Q5ZUA2 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 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 | 853 | 0.83 | 0.85 | 87 | MG, ANP |
| 2 | 243 | 0.72 | 0.87 | 39 | ANP, MG |
| 3 | 191 | 0.55 | 0.79 | 31 | MES, CL |
| 4 | 208 | 0.53 | 0.78 | 26 | MES |
| 5 | 91 | 0.47 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1536 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4BRD · Legionella pneumophila NTPDase1 Q193E crystal form II, closed, Mg AMPPNP complex · 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 4BRD · PDBe 4BRD · UniProt Q5ZUA2
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