MolNFT v1 · #119133 · protein
Crystal structure of human CD45 extracellular region, domains D1-D4
5FMV · Receptor-type tyrosine-protein phosphatase C: “Crystal structure of human CD45 extracellular region, domains D1-D4”. X-ray diffraction, 2 ligands (NAG, SO4), 5 pockets (best druggability 0.66). MolNFT v1 #119133 on GenesisL1: 3D…
- PDB
- 5FMV
- Type
- protein
- Length
- 698 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
- P08575
- Ligands
- NAG, SO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase C (EC 3.1.3.48) | protein | 351 | 4% helix, 51% strand | P08575 |
| B | Receptor-type tyrosine-protein phosphatase C (EC 3.1.3.48) | protein | 347 | 3% helix, 51% strand | P08575 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.66 | 0.77 | 60 | NAG |
| 2 | 177 | 0.48 | 0.76 | 30 | empty |
| 3 | 172 | 0.43 | 0.74 | 22 | NAG |
| 4 | 62 | 0.34 | 0.77 | 12 | empty |
| 5 | 54 | 0.32 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 950 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 5FMV · Crystal structure of human CD45 extracellular region, domains d1-d4 · the same entry in another collection · chain A against A, TM-score 1.00
- P08575 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase C… · a predicted model of the same protein · chain B against A, TM-score 0.87
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 P08575
- Elsewhere: RCSB PDB 5FMV · PDBe 5FMV · UniProt P08575
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