Research workbench
Crystal structure of human phosphatase pten treated with a bisperoxovanadium complex
Analyse Crystal structure of human phosphatase pten treated with a bisperoxovanadium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BZX
- Type
- protein
- Length
- 1,256 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein…
- EC
- 3.1.3.16, 3.1.3.48, 3.1.3.67
- UniProt
- P60484
- Ligands
- VO4
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase pten (EC 3.1.3.16, 3.1.3.48, 3.1.3.67) | protein | 314 | 26% helix, 31% strand | P60484 |
Ligands and binding sites
- VO4 · Vanadate ion · ion · 2 copies · chains A, C
- TLA · L(+)-tartaric acid · additive · 3 copies · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.75 | 0.79 | 98 | empty |
| 2 | 997 | 0.75 | 0.78 | 99 | empty |
| 3 | 107 | 0.47 | 0.80 | 25 | TLA, VO4 |
| 4 | 68 | 0.45 | 0.82 | 15 | TLA |
| 5 | 141 | 0.45 | 0.76 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–D · 673 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 625 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 398 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 94 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 42 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5BZX · Crystal structure of human phosphatase PTEN treated with a bisperoxovanadium complex · the same entry in another collection · chain A against A, TM-score 1.00
- P60484 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3,4,5-trisphosphate… · 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 P60484
- Elsewhere: RCSB PDB 5BZX · PDBe 5BZX · UniProt P60484
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