Research workbench
Crystal structure of SOCS2:ELONGIN C:ELONGIN B in complex with erythropoietin receptor peptide
Analyse Crystal structure of SOCS2:ELONGIN C:ELONGIN B in complex with erythropoietin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I4X
- Type
- protein
- Length
- 356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongin-B; Elongin-C; Suppressor of cytokine signaling 2; Erythropoietin receptor
- UniProt
- Q15370, Q15369, O14508
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Elongin-B | protein | 103 | 15% helix, 39% strand | Q15370 |
| C | Elongin-C | protein | 86 | 45% helix, 15% strand | Q15369 |
| A | Suppressor of cytokine signaling 2 | protein | 158 | 32% helix, 19% strand | O14508 |
| D | Erythropoietin receptor | protein | 9 | 0% helix, 22% strand | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.46 | 0.81 | 21 | empty |
| 2 | 52 | 0.34 | 0.79 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1127 Ų buried · 14 hydrogen bonds · protein-protein
- C–A · 1056 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 558 Ų buried · 13 hydrogen bonds · protein-protein
- B–A · 201 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 modified (artifact, phosphorylation).
Compared structures
- 6I4X · Crystal structure of SOCS2:Elongin C:Elongin B in complex with erythropoietin receptor… · the same entry in another collection · chain B against B, TM-score 1.00
- Q15370 · AlphaFold monomer V2.0 prediction for elongin-B (Q15370) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · a predicted model of the same protein · chain C against A, TM-score 0.98
- O14508 · AlphaFold monomer V2.0 prediction for suppressor of cytokine signaling 2 (O14508) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q15370
- Every structure of UniProt Q15369
- Every structure of UniProt O14508
- Elsewhere: RCSB PDB 6I4X · PDBe 6I4X · UniProt Q15370 · UniProt Q15369 · UniProt O14508
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