Research workbench
NTPDase1 in complex with Heptamolybdate
Analyse NTPDase1 in complex with Heptamolybdate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZX0
- Type
- protein
- Length
- 1,561 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- RATTUS NORVEGICUS
- Molecule
- Ectonucleoside triphosphate diphosphohydrolase 1
- EC
- 3.6.1.5
- UniProt
- P97687
- Ligands
- MO7, NA, CL
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.5 · 4 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) | protein | 385 | 41% helix, 24% strand | P97687 |
| B | Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) | protein | 386 | 44% helix, 24% strand | P97687 |
| C | Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) | protein | 393 | 43% helix, 24% strand | P97687 |
| D | Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) | protein | 397 | 42% helix, 23% strand | P97687 |
Ligands and binding sites
- MO7 · bis(mu4-oxo)-bis(mu3-oxo)-octakis(mu2-oxo)-dodecaoxo-heptamolybdenum (VI) · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains B, C, D
- CL · Chloride ion · ion · 22 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.83 | 0.83 | 130 | CL |
| 2 | 1194 | 0.82 | 0.83 | 118 | CL |
| 3 | 1153 | 0.80 | 0.82 | 101 | empty |
| 4 | 672 | 0.79 | 0.84 | 68 | CL |
| 5 | 618 | 0.74 | 0.81 | 69 | CL |
Interfaces
3 interfaces between chains.
- B–C · 1253 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 937 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 694 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
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 P97687
- Elsewhere: RCSB PDB 3ZX0 · PDBe 3ZX0 · UniProt P97687
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