MolNFT v1 · #55200 · protein
Crystal structure of the N-terminal IG1-2 module of human receptor protein tyrosine phosphatase sigma
2YD2 · Receptor-type tyrosine-protein phosphatase S: “Crystal structure of the N-terminal IG1-2 module of human receptor protein tyrosine phosphatase sigma”. X-ray diffraction, 2 ligands (IOD, CL), 3 pockets (best druggability 0.47).…
- PDB
- 2YD2
- Type
- protein
- Length
- 197 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
- IOD, CL
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase S (EC 3.1.3.48) | protein | 197 | 5% helix, 53% strand | Q13332 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.47 | 0.79 | 16 | IOD |
| 2 | 98 | 0.38 | 0.75 | 17 | empty |
| 3 | 52 | 0.29 | 0.74 | 14 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2YD2 · Crystal structure of the N-terminal Ig1-2 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 0.96
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 2YD2 · PDBe 2YD2 · UniProt Q13332
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