Research workbench
Crystal structure of the his domain protein tyrosine phosphatase (hd- PTP/PTPN23) BRO1 domain (CHMP4A 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
- 5MK1
- Type
- protein
- Length
- 1,480 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 4A
- EC
- 3.1.3.48
- UniProt
- Q9H3S7, Q9BY43
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48) | protein | 358 | 67% helix, 3% strand | Q9H3S7 |
| C | Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48) | protein | 361 | 66% helix, 3% strand | Q9H3S7 |
| D | Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48) | protein | 359 | 67% helix, 3% strand | Q9H3S7 |
| E, F, H, K | Charged multivesicular body protein 4A | protein | 11 | 73% helix, 0% strand | Q9BY43 |
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 866 | 0.76 | 0.79 | 101 | empty |
| 2 | 1194 | 0.70 | 0.75 | 122 | empty |
| 3 | 504 | 0.68 | 0.79 | 62 | empty |
| 4 | 408 | 0.67 | 0.79 | 41 | empty |
| 5 | 559 | 0.62 | 0.75 | 68 | empty |
Interfaces
11 interfaces between chains.
- A–C · 732 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 682 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 667 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 609 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 576 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5MK1 · Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1… · the same entry in another collection · chain K against K, 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 D against A, TM-score 1.00
- Q9BY43 · AlphaFold monomer V2.0 prediction for charged multivesicular body protein 4A (Q9BY43) · a predicted model of the same protein · chain F against A, TM-score 0.79
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 Q9BY43
- Elsewhere: RCSB PDB 5MK1 · PDBe 5MK1 · UniProt Q9H3S7 · UniProt Q9BY43
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