Research workbench
Crystal structure of JNK1 bound to a MKK7 docking motif
Analyse Crystal structure of JNK1 bound to a MKK7 docking motif in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UX9
- Type
- protein
- Length
- 1,386 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 8; Dual specificity mitogen-activated protein kinase…
- EC
- 2.7.11.24
- UniProt
- P45983, O14733
- Ligands
- ANP, SO4
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 8 (EC 2.7.11.24) | protein | 343 | 38% helix, 17% strand | P45983 |
| B | Mitogen-activated protein kinase 8 (EC 2.7.11.24) | protein | 327 | 40% helix, 18% strand | P45983 |
| C | Mitogen-activated protein kinase 8 (EC 2.7.11.24) | protein | 333 | 41% helix, 18% strand | P45983 |
| D | Mitogen-activated protein kinase 8 (EC 2.7.11.24) | protein | 344 | 39% helix, 16% strand | P45983 |
| F | Dual specificity mitogen-activated protein kinase kinase 7 | protein | 10 | 0% helix, 0% strand | O14733 |
| G | Dual specificity mitogen-activated protein kinase kinase 7 | protein | 8 | 0% helix, 0% strand | O14733 |
| H | Dual specificity mitogen-activated protein kinase kinase 7 | protein | 12 | 0% helix, 0% strand | O14733 |
| I | Dual specificity mitogen-activated protein kinase kinase 7 | protein | 9 | 0% helix, 0% strand | O14733 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, D, C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.87 | 0.88 | 84 | SO4 |
| 2 | 414 | 0.80 | 0.88 | 38 | empty |
| 3 | 802 | 0.76 | 0.80 | 101 | ANP, SO4 |
| 4 | 595 | 0.73 | 0.80 | 45 | empty |
| 5 | 500 | 0.69 | 0.79 | 52 | ANP, SO4 |
Interfaces
10 interfaces between chains.
- A–D · 795 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 792 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 724 Ų buried · 7 hydrogen bonds · protein-protein
- D–I · 715 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 616 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4UX9 · Crystal structure of JNK1 bound to a MKK7 docking motif · the same entry in another collection · chain I against I, TM-score 1.00
- P45983 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase 8 (P45983) · 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 P45983
- Every structure of UniProt O14733
- Elsewhere: RCSB PDB 4UX9 · PDBe 4UX9 · UniProt P45983 · UniProt O14733
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