MolNFT v1 · #87127 · protein
Legionella pneumophila NTPDASE1 crystal form II (closed) in complex with mg umppnp
4BRI · Ectonucleoside triphosphate diphosphohydrolase I: “Legionella pneumophila NTPDASE1 crystal form II (closed) in complex with mg umppnp”. X-ray diffraction, 3 ligands (UNP, MG, CL), 9 pockets (best druggability 0.85). MolNFT v1 #87127…
- PDB
- 4BRI
- Type
- protein
- Length
- 716 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
- UNP, MG, CL
- Pockets
- 9 · best druggability 0.85
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 | 357 | 39% helix, 25% strand | Q5ZUA2 |
Ligands and binding sites
- UNP · 5'-O-[(R)-hydroxy{[(s)-hydroxy(phosphonoamino) phosphoryl]oxy}phosphoryl]uridine · 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.85 | 0.86 | 115 | UNP, MG |
| 2 | 192 | 0.55 | 0.79 | 26 | MES, CL |
| 3 | 212 | 0.53 | 0.78 | 29 | MES |
| 4 | 100 | 0.48 | 0.80 | 21 | empty |
| 5 | 67 | 0.45 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1520 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4BRI · Legionella pneumophila NTPDase1 crystal form II (closed) in complex with MG UMPPNP · 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 4BRI · PDBe 4BRI · UniProt Q5ZUA2
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