Research workbench
Crystal structure of the N-terminal IG1-3 module of human receptor protein tyrosine phosphatase sigma
Analyse Crystal structure of the N-terminal IG1-3 module 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
- 2YD9
- Type
- protein
- Length
- 278 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, CL, IOD
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase S (EC 3.1.3.48) | protein | 278 | 4% helix, 53% strand | Q13332 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CL · Chloride ion · ion · 4 copies · chains A
- IOD · Iodide ion · ion · 4 copies · chains A
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.52 | 0.78 | 26 | CL |
| 2 | 79 | 0.33 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2YD9 · Crystal structure of the N-terminal Ig1-3 module 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 0.74
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 2YD9 · PDBe 2YD9 · UniProt Q13332
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