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Crystal structure and domain rotation of NTPDASE1 CD39
Analyse Crystal structure and domain rotation of NTPDASE1 CD39 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZX3
- Type
- protein
- Length
- 1,589 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleoside triphosphate diphosphohydrolase 1
- EC
- 3.6.1.5
- UniProt
- P97687
- Ligands
- NA, CL
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) | protein | 399 | 41% helix, 24% strand | P97687 |
| B | Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) | protein | 400 | 42% helix, 24% strand | P97687 |
| C | Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) | protein | 393 | 42% helix, 23% strand | P97687 |
| D | Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) | protein | 397 | 41% helix, 24% strand | P97687 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains B, C, D
- CL · Chloride ion · ion · 27 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
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 759 | 0.84 | 0.87 | 82 | CL |
| 2 | 990 | 0.84 | 0.85 | 121 | CL |
| 3 | 393 | 0.81 | 0.90 | 57 | CL |
| 4 | 859 | 0.81 | 0.83 | 85 | CL |
| 5 | 722 | 0.75 | 0.80 | 68 | CL |
Interfaces
3 interfaces between chains.
- B–C · 1194 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 937 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 929 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 3ZX3 · Crystal Structure and Domain Rotation of NTPDase1 CD39 · the same entry in another collection · chain D against D, TM-score 1.00
- P97687 · AlphaFold monomer V2.0 prediction for ectonucleoside triphosphate diphosphohydrolase 1… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 3ZX3 · PDBe 3ZX3 · UniProt P97687
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