MolNFT v1 · #103278 · protein
Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with trkc
4PBW · Nt-3 growth factor receptor: “Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with trkc”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.79). MolNFT v1 #103278 on GenesisL1: 3D…
- PDB
- 4PBW
- Type
- protein
- Length
- 1,359 residues
- Chains
- 6
- 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
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Nt-3 growth factor receptor (EC 2.7.10.1) | protein | 262 | 16% helix, 34% strand | Q91044 |
| A | Nt-3 growth factor receptor (EC 2.7.10.1) | protein | 263 | 16% helix, 33% strand | Q91044 |
| C | Nt-3 growth factor receptor (EC 2.7.10.1) | protein | 255 | 14% helix, 34% strand | Q91044 |
| D | Protein-tyrosine phosphatase CRYPALPHA1 isoform | protein | 193 | 3% helix, 54% strand | Q90815 |
| E | Protein-tyrosine phosphatase CRYPALPHA1 isoform | protein | 194 | 3% helix, 54% strand | Q90815 |
| F | Protein-tyrosine phosphatase CRYPALPHA1 isoform | protein | 192 | 3% helix, 53% strand | Q90815 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.79 | 0.81 | 94 | empty |
| 2 | 576 | 0.73 | 0.81 | 59 | empty |
| 3 | 92 | 0.58 | 0.87 | 21 | empty |
| 4 | 235 | 0.57 | 0.79 | 38 | empty |
| 5 | 266 | 0.54 | 0.76 | 39 | empty |
Interfaces
7 interfaces between chains.
- B–E · 1298 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1291 Ų buried · 24 hydrogen bonds · protein-protein
- C–F · 1179 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1171 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 684 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4PBW · Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with… · the same entry in another collection · chain F against F, 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 C 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 4PBW · PDBe 4PBW · UniProt Q91044 · UniProt Q90815
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