Research workbench
Crystal structure of the N-terminal IG1-2 module of human receptor protein tyrosine phosphatase lar in complex with sucrose octasulphate
Analyse Crystal structure of the N-terminal IG1-2 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
- 2YD8
- Type
- protein
- Length
- 198 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-type tyrosine-protein phosphatase F
- EC
- 3.1.3.48
- UniProt
- P10586
- Ligands
- YYJ
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase F (EC 3.1.3.48) | protein | 198 | 8% helix, 55% strand | P10586 |
Ligands and binding sites
- YYJ · 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose · ligand · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.50 | 0.76 | 25 | empty |
| 2 | 86 | 0.33 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2YD8 · 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
- P10586 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase F… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P10586
- Elsewhere: RCSB PDB 2YD8 · PDBe 2YD8 · UniProt P10586
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