MolNFT v1 · #87125 · protein
Legionella pneumophila NTPDASE1 crystal form II (closed) in complex with mg gmppnp
4BRG · Ectonucleoside triphosphate diphosphohydrolase I: “Legionella pneumophila NTPDASE1 crystal form II (closed) in complex with mg gmppnp”. X-ray diffraction, 4 ligands (GNP, MG, NA), 10 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 4BRG
- 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
- GNP, MG, NA, CL
- Pockets
- 10 · best druggability 0.82
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 | 361 | 40% helix, 25% strand | Q5ZUA2 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 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
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.82 | 0.83 | 90 | GNP, MG |
| 2 | 324 | 0.72 | 0.85 | 45 | GNP, MG |
| 3 | 186 | 0.56 | 0.80 | 28 | MES, CL |
| 4 | 199 | 0.52 | 0.77 | 25 | MES |
| 5 | 111 | 0.47 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1575 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4BRG · Legionella pneumophila NTPDase1 crystal form II (closed) in complex with MG GMPPNP · 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 4BRG · PDBe 4BRG · UniProt Q5ZUA2
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