Research workbench
Crystal structure of PDZ1 domain of human protein tyrosine phosphatase ptp-bas
Analyse Crystal structure of PDZ1 domain of human protein tyrosine phosphatase ptp-bas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GLJ
- Type
- protein
- Length
- 379 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 13
- EC
- 3.1.3.48
- UniProt
- Q12923
- Ligands
- CL
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Tyrosine-protein phosphatase non-receptor type 13 (EC 3.1.3.48) | protein | 96 | 16% helix, 35% strand | Q12923 |
| B | Tyrosine-protein phosphatase non-receptor type 13 (EC 3.1.3.48) | protein | 93 | 16% helix, 37% strand | Q12923 |
| C | Tyrosine-protein phosphatase non-receptor type 13 (EC 3.1.3.48) | protein | 94 | 16% helix, 36% strand | Q12923 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.56 | 0.75 | 49 | CL |
| 2 | 138 | 0.39 | 0.74 | 25 | empty |
| 3 | 78 | 0.33 | 0.75 | 27 | CL |
| 4 | 63 | 0.33 | 0.76 | 12 | empty |
| 5 | 58 | 0.31 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1071 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 910 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 619 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 170 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 118 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5GLJ · Crystal Structure of PDZ1 Domain of Human Protein Tyrosine Phosphatase PTP-Bas · the same entry in another collection · chain A against A, TM-score 1.00
- Q12923 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type 13… · a predicted model of the same protein · chain C against A, TM-score 0.87
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 Q12923
- Elsewhere: RCSB PDB 5GLJ · PDBe 5GLJ · UniProt Q12923
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