MolNFT v1 · #103277 · protein
Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with trkc
4PBV · Nt-3 growth factor receptor: “Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with trkc”. X-ray diffraction, 2 ligands (NAG, SO4), 20 pockets (best druggability 0.75). MolNFT v1 #103277 on…
- PDB
- 4PBV
- Type
- protein
- Length
- 1,095 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nt-3 growth factor receptor; Protein-tyrosine phosphatase CRYPALPHA1 isoform
- EC
- 2.7.10.1
- UniProt
- Q91044, Q90815
- Ligands
- NAG, SO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nt-3 growth factor receptor (EC 2.7.10.1) | protein | 257 | 14% helix, 35% strand | Q91044 |
| B | Nt-3 growth factor receptor (EC 2.7.10.1) | protein | 254 | 14% helix, 35% strand | Q91044 |
| C | Protein-tyrosine phosphatase CRYPALPHA1 isoform | protein | 195 | 6% helix, 55% strand | Q90815 |
| D | Protein-tyrosine phosphatase CRYPALPHA1 isoform | protein | 195 | 6% helix, 55% strand | Q90815 |
| E | Protein-tyrosine phosphatase CRYPALPHA1 isoform | protein | 194 | 5% helix, 55% strand | Q90815 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.75 | 0.82 | 56 | empty |
| 2 | 665 | 0.75 | 0.81 | 84 | empty |
| 3 | 62 | 0.71 | 0.97 | 22 | empty |
| 4 | 246 | 0.63 | 0.81 | 43 | empty |
| 5 | 369 | 0.60 | 0.77 | 40 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1270 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1180 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1154 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 589 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 117 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4PBV · Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- Q91044 · AlphaFold monomer V2.0 prediction for nt-3 growth factor receptor (Q91044) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q91044
- Every structure of UniProt Q90815
- Elsewhere: RCSB PDB 4PBV · PDBe 4PBV · UniProt Q91044 · UniProt Q90815
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