Research workbench
Legionella pneumophila NTPDASE1 crystal form II, closed, in complex with two phosphates bound to active site mg and product AMP
Analyse Legionella pneumophila NTPDASE1 crystal form II, closed, in complex with two… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BRQ
- Type
- protein
- Length
- 718 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
- AMP, MG, PO4, CL
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ectonucleoside triphosphate diphosphohydrolase I (EC 3.6.1.5) | protein | 359 | 40% helix, 25% strand | Q5ZUA2 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 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 | 1088 | 0.83 | 0.84 | 99 | AMP, PO4, MG |
| 2 | 315 | 0.71 | 0.85 | 44 | AMP, PO4, MG |
| 3 | 245 | 0.59 | 0.80 | 28 | MES |
| 4 | 201 | 0.57 | 0.80 | 27 | MES, CL |
| 5 | 157 | 0.47 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1558 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4BRQ · Legionella pneumophila NTPDASE1 crystal form II, closed, in complex with two phosphates… · 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 4BRQ · PDBe 4BRQ · UniProt Q5ZUA2
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