Research workbench
Crystal structure of inhibitory protein SOCS3 in complex with JAK2 kinase domain and fragment of GP130 intracellular domain
Analyse Crystal structure of inhibitory protein SOCS3 in complex with JAK2 kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GL9
- Type
- protein
- Length
- 1,667 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase; Interleukin-6 receptor subunit beta; Suppressor of cytokine…
- EC
- 2.7.10.2
- UniProt
- G5E852, Q00560, O35718
- Ligands
- IZA, PO4
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Tyrosine-protein kinase (EC 2.7.10.2) | protein | 284 | 39% helix, 20% strand | G5E852 |
| B | Tyrosine-protein kinase (EC 2.7.10.2) | protein | 282 | 39% helix, 21% strand | G5E852 |
| I, K, L | Interleukin-6 receptor subunit beta | protein | 8 | 0% helix, 38% strand | Q00560 |
| J | Interleukin-6 receptor subunit beta | protein | 9 | 0% helix, 33% strand | Q00560 |
| E | Suppressor of cytokine signaling 3,SUPPRESSOR of cytokine signaling 3,SUPPRESSOR of cytokine signaling 3,SUPPRESSOR of cytokine signaling 3 | protein | 124 | 26% helix, 29% strand | O35718 |
| F | Suppressor of cytokine signaling 3,SUPPRESSOR of cytokine signaling 3,SUPPRESSOR of cytokine signaling 3,SUPPRESSOR of cytokine signaling 3 | protein | 126 | 25% helix, 29% strand | O35718 |
| G, H | Suppressor of cytokine signaling 3,SUPPRESSOR of cytokine signaling 3,SUPPRESSOR of cytokine signaling 3,SUPPRESSOR of cytokine signaling 3 | protein | 125 | 26% helix, 29% strand | O35718 |
Ligands and binding sites
- IZA · 2-tert-butyl-9-fluoro-3,6-dihydro-7H-benz[h]-imidaz[4,5-f]isoquinoline-7-one · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.81 | 0.82 | 96 | PO4, IZA |
| 2 | 453 | 0.78 | 0.86 | 41 | empty |
| 3 | 445 | 0.76 | 0.85 | 48 | IZA |
| 4 | 603 | 0.73 | 0.80 | 68 | IZA |
| 5 | 464 | 0.70 | 0.80 | 57 | IZA |
Interfaces
17 interfaces between chains.
- A–E · 1026 Ų buried · 18 hydrogen bonds · protein-protein
- B–H · 1022 Ų buried · 16 hydrogen bonds · protein-protein
- C–G · 1021 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1021 Ų buried · 17 hydrogen bonds · protein-protein
- J–F · 854 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (phosphorylation).
Compared structures
- 4GL9 · Crystal structure of inhibitory protein SOCS3 in complex with JAK2 kinase domain and… · the same entry in another collection · chain H against H, TM-score 1.00
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 G5E852
- Every structure of UniProt Q00560
- Every structure of UniProt O35718
- Elsewhere: RCSB PDB 4GL9 · PDBe 4GL9 · UniProt G5E852 · UniProt Q00560 · UniProt O35718
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