Research workbench
Crystal structure of the his domain protein tyrosine phosphatase (hd- PTP/PTPN23) BRO1 domain (endofin peptide complex)
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
- 5MK0
- Type
- protein
- Length
- 753 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 23; Zinc finger fyve domain-containing…
- EC
- 3.1.3.48
- UniProt
- Q9H3S7, Q7Z3T8
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 67% 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 | 361 | 66% helix, 3% strand | Q9H3S7 |
| B | Zinc finger fyve domain-containing protein 16 | protein | 20 | 90% helix, 0% strand | Q7Z3T8 |
| C | Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48) | protein | 359 | 67% helix, 3% strand | Q9H3S7 |
| D | Zinc finger fyve domain-containing protein 16 | protein | 13 | 85% helix, 0% strand | Q7Z3T8 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.78 | 0.80 | 95 | empty |
| 2 | 78 | 0.60 | 0.89 | 22 | empty |
| 3 | 116 | 0.55 | 0.83 | 25 | empty |
| 4 | 150 | 0.52 | 0.79 | 34 | empty |
| 5 | 105 | 0.42 | 0.77 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 862 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 622 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 589 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 441 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 254 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5MK0 · Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1… · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.99
- Q7Z3T8 · AlphaFold monomer V2.0 prediction for zinc finger fyve domain- containing protein 16… · a predicted model of the same protein · chain D against A, TM-score 0.72
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 Q7Z3T8
- Elsewhere: RCSB PDB 5MK0 · PDBe 5MK0 · UniProt Q9H3S7 · UniProt Q7Z3T8
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