Research workbench
Crystal structure of rat CD45 extracellular region, domains D3-D4
Analyse Crystal structure of rat CD45 extracellular region, domains D3-D4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FN8
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-type tyrosine-protein phosphatase C
- EC
- 3.1.3.48
- UniProt
- P04157
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Receptor-type tyrosine-protein phosphatase C (EC 3.1.3.48) | protein | 178 | 0% helix, 34% strand | P04157 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- FLC · Citrate anion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.52 | 0.75 | 24 | empty |
| 2 | 234 | 0.52 | 0.76 | 28 | empty |
| 3 | 101 | 0.43 | 0.78 | 21 | NAG |
| 4 | 76 | 0.39 | 0.78 | 13 | empty |
| 5 | 93 | 0.35 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 486 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5FN8 · Crystal structure of rat CD45 extracellular region, domains d3-d4 · the same entry in another collection · chain A against A, TM-score 1.00
- P04157 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase C… · a predicted model of the same protein · chain A against A, TM-score 0.73
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 P04157
- Elsewhere: RCSB PDB 5FN8 · PDBe 5FN8 · UniProt P04157
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