MolNFT v1 · #87123 · protein
Legionella pneumophila NTPDASE1 crystal form II (closed) in complex with transition state mimic adenosine 5' phosphovanadate
4BRE · Ectonucleoside triphosphate diphosphohydrolase I: “Legionella pneumophila NTPDASE1 crystal form II (closed) in complex with transition state mimic adenosine 5'…”. X-ray diffraction, 3 ligands (50T, MG, NA), 10 pockets (best…
- PDB
- 4BRE
- Type
- protein
- Length
- 716 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleoside triphosphate diphosphohydrolase I
- UniProt
- Q5ZUA2
- Ligands
- 50T, MG, NA
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ectonucleoside triphosphate diphosphohydrolase I | protein | 358 | 41% helix, 25% strand | Q5ZUA2 |
Ligands and binding sites
- 50T · Adenosine-5'-phosphovanadate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 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 | 1173 | 0.83 | 0.84 | 99 | MG, 50T |
| 2 | 283 | 0.74 | 0.87 | 38 | 50T, MG |
| 3 | 210 | 0.58 | 0.80 | 23 | MES |
| 4 | 198 | 0.56 | 0.80 | 25 | MES |
| 5 | 140 | 0.47 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1554 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4BRE · Legionella pneumophila NTPDase1 crystal form II (closed) in complex with transition state… · 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 4BRE · PDBe 4BRE · UniProt Q5ZUA2
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