MolNFT v1 · #111060 · protein
Crystal structure of ptp delta MEA3/MEB minus variant IG1-FN1
4YFG · Receptor-type tyrosine-protein phosphatase delta: “Crystal structure of ptp delta MEA3/MEB minus variant IG1-FN1”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.58). MolNFT v1 #111060 on GenesisL1: 3D structure…
- PDB
- 4YFG
- Type
- protein
- Length
- 962 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-type tyrosine-protein phosphatase delta
- EC
- 3.1.3.48
- UniProt
- Q64487
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Receptor-type tyrosine-protein phosphatase delta (EC 3.1.3.48) | protein | 481 | 2% helix, 51% strand | Q64487 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.58 | 0.77 | 41 | empty |
| 2 | 187 | 0.49 | 0.76 | 36 | empty |
| 3 | 156 | 0.45 | 0.76 | 26 | empty |
| 4 | 133 | 0.44 | 0.77 | 23 | empty |
| 5 | 85 | 0.34 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- B–A · 1692 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4YFG · Crystal structure of PTP delta meA3/meB minus variant Ig1-Fn1 · the same entry in another collection · chain B against B, TM-score 1.00
- Q64487 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase delta… · a predicted model of the same protein · chain B against A, TM-score 0.41
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 Q64487
- Elsewhere: RCSB PDB 4YFG · PDBe 4YFG · UniProt Q64487
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