Research workbench
Crystal structure of the his domain protein tyrosine phosphatase (hd- PTP/PTPN23) BRO1 domain (CHMP4B peptide complex structure)
Analyse Crystal structure of the his domain protein tyrosine phosphatase (hd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MK2
- Type
- protein
- Length
- 727 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 23; Charged multivesicular body protein 4B
- EC
- 3.1.3.48
- UniProt
- Q9H3S7, Q9H444
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48) | protein | 355 | 66% helix, 3% strand | Q9H3S7 |
| B | Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48) | protein | 361 | 65% helix, 3% strand | Q9H3S7 |
| C | Charged multivesicular body protein 4B | protein | 11 | 82% helix, 0% strand | Q9H444 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.70 | 0.76 | 72 | empty |
| 2 | 495 | 0.65 | 0.77 | 47 | empty |
| 3 | 123 | 0.45 | 0.77 | 20 | empty |
| 4 | 116 | 0.43 | 0.76 | 20 | empty |
| 5 | 97 | 0.38 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 795 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 570 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 65 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5MK2 · Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H3S7 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type 23… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9H444 · AlphaFold monomer V2.0 prediction for charged multivesicular body protein 4B (Q9H444) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 Q9H3S7
- Every structure of UniProt Q9H444
- Elsewhere: RCSB PDB 5MK2 · PDBe 5MK2 · UniProt Q9H3S7 · UniProt Q9H444
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