MolNFT v1 · #87126 · protein
Legionella pneumophila NTPDASE1 crystal form II (closed) in complex with mg and thiamine phosphovanadate
4BRH · Ectonucleoside triphosphate diphosphohydrolase I: “Legionella pneumophila NTPDASE1 crystal form II (closed) in complex with mg and thiamine phosphovanadate”. X-ray diffraction, 4 ligands (TMV, DVT, MG), 8 pockets (best druggability…
- PDB
- 4BRH
- Type
- protein
- Length
- 720 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
- TMV, DVT, MG, CL
- Pockets
- 8 · best druggability 0.80
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 | 361 | 40% helix, 25% strand | Q5ZUA2 |
| B | Ectonucleoside triphosphate diphosphohydrolase I (EC 3.6.1.5) | protein | 359 | 40% helix, 26% strand | Q5ZUA2 |
Ligands and binding sites
- TMV · Thiamine-phosphovanadate · ligand · 2 copies · chains A, B
- DVT · Decavanadate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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
- GOL · Glycerol · additive · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.80 | 0.82 | 82 | empty |
| 2 | 307 | 0.74 | 0.87 | 42 | TMV, MG |
| 3 | 295 | 0.73 | 0.87 | 44 | TMV, MG |
| 4 | 230 | 0.57 | 0.79 | 26 | MES |
| 5 | 213 | 0.56 | 0.79 | 23 | MES |
Interfaces
1 interface between chains.
- A–B · 1524 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4BRH · Legionella pneumophila NTPDase1 crystal form II (closed) in complex with MG AND THIAMINE… · 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 4BRH · PDBe 4BRH · UniProt Q5ZUA2
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