Research workbench
Crystal structure of the his domain protein tyrosine phosphatase (hd- PTP/PTPN23) bro 1 domain (CHMP4C 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
- 5MK3
- Type
- protein
- Length
- 1,487 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 23; Charged multivesicular body protein 4C
- EC
- 3.1.3.48
- UniProt
- Q9H3S7, Q96CF2
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48) | protein | 361 | 67% helix, 2% strand | Q9H3S7 |
| E, F, H | Charged multivesicular body protein 4C | protein | 11 | 82% helix, 0% strand | Q96CF2 |
| G | Charged multivesicular body protein 4C | protein | 10 | 80% helix, 0% strand | Q96CF2 |
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.74 | 0.77 | 123 | empty |
| 2 | 335 | 0.59 | 0.77 | 49 | empty |
| 3 | 210 | 0.55 | 0.78 | 32 | empty |
| 4 | 167 | 0.52 | 0.79 | 25 | empty |
| 5 | 179 | 0.51 | 0.78 | 23 | empty |
Interfaces
13 interfaces between chains.
- B–F · 581 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 575 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 572 Ų buried · 6 hydrogen bonds · protein-protein
- D–H · 567 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 494 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5MK3 · Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro 1… · the same entry in another collection · chain H against H, 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 A against A, TM-score 0.99
- Q96CF2 · AlphaFold monomer V2.0 prediction for charged multivesicular body protein 4C (Q96CF2) · a predicted model of the same protein · chain G against A, TM-score 0.86
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 Q96CF2
- Elsewhere: RCSB PDB 5MK3 · PDBe 5MK3 · UniProt Q9H3S7 · UniProt Q96CF2
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