Research workbench
Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with trkc
Analyse Crystal structure of chicken receptor protein tyrosine phosphatase sigma in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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