Research workbench
Human receptor protein tyrosine phosphatase gamma, domain 1, in complex with 3-[(3,4-DICHLOROBENZYL)SULFANYL]THIOPHENE-2-carboxylic acid via soaking
Analyse Human receptor protein tyrosine phosphatase gamma, domain 1, in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QCE
- Type
- protein
- Length
- 572 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-type tyrosine-protein phosphatase gamma
- EC
- 3.1.3.48
- UniProt
- P23470
- Ligands
- NXY, SO4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase gamma (EC 3.1.3.48) | protein | 288 | 37% helix, 24% strand | P23470 |
| B | Receptor-type tyrosine-protein phosphatase gamma (EC 3.1.3.48) | protein | 284 | 39% helix, 24% strand | P23470 |
Ligands and binding sites
- NXY · 3-[(3,4-dichlorobenzyl)sulfanyl]thiophene-2-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.73 | 0.80 | 48 | empty |
| 2 | 138 | 0.63 | 0.85 | 16 | NXY |
| 3 | 375 | 0.57 | 0.75 | 37 | empty |
| 4 | 51 | 0.36 | 0.80 | 14 | empty |
| 5 | 75 | 0.35 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 407 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3QCE · Human receptor protein tyrosine phosphatase gamma, domain 1, in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P23470 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase gamma… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P23470
- Elsewhere: RCSB PDB 3QCE · PDBe 3QCE · UniProt P23470
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