Research workbench
Crystal structure of the six N-terminal domains of human receptor protein tyrosine phosphatase sigma
Analyse Crystal structure of the six N-terminal domains of human receptor protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PBX
- Type
- protein
- Length
- 568 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-type tyrosine-protein phosphatase S
- EC
- 3.1.3.48
- UniProt
- Q13332
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase S (EC 3.1.3.48) | protein | 568 | 2% helix, 48% strand | Q13332 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.67 | 0.86 | 33 | empty |
| 2 | 288 | 0.57 | 0.77 | 38 | empty |
| 3 | 66 | 0.51 | 0.85 | 16 | empty |
| 4 | 104 | 0.42 | 0.77 | 16 | empty |
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4PBX · Crystal structure of the six N-terminal domains of human receptor protein tyrosine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13332 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase S… · a predicted model of the same protein · chain A against A, TM-score 0.44
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 Q13332
- Elsewhere: RCSB PDB 4PBX · PDBe 4PBX · UniProt Q13332
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