Research workbench
Crystal structure of the complex between carbonic anhydrase-like domain of ptprg and immunoglobulin domains 2-3 of CNTN3
Analyse Crystal structure of the complex between carbonic anhydrase-like domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E5R
- Type
- protein
- Length
- 901 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-type tyrosine-protein phosphatase gamma; Contactin-3
- EC
- 3.1.3.48
- UniProt
- P23470, Q07409
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase gamma (EC 3.1.3.48) | protein | 258 | 18% helix, 31% strand | P23470 |
| B | Contactin-3 | protein | 187 | 5% helix, 51% strand | Q07409 |
| C | Receptor-type tyrosine-protein phosphatase gamma (EC 3.1.3.48) | protein | 264 | 16% helix, 33% strand | P23470 |
| D | Contactin-3 | protein | 192 | 5% helix, 47% strand | Q07409 |
Ligands and binding sites
- MLI · Malonate ion · additive · 3 copies · chains A, C, D
- FMT · Formic acid · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.68 | 0.90 | 25 | empty |
| 2 | 246 | 0.56 | 0.78 | 32 | FMT |
| 3 | 247 | 0.53 | 0.76 | 31 | empty |
| 4 | 224 | 0.53 | 0.76 | 28 | empty |
| 5 | 206 | 0.52 | 0.77 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 886 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 879 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 492 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5E5R · Crystal structure of the complex between Carbonic anhydrase-like domain of PTPRG and… · the same entry in another collection · chain D against D, TM-score 1.00
- P23470 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase gamma… · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q07409 · AlphaFold monomer V2.0 prediction for contactin-3 (Q07409) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P23470
- Every structure of UniProt Q07409
- Elsewhere: RCSB PDB 5E5R · PDBe 5E5R · UniProt P23470 · UniProt Q07409
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