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Structure of the human mitogen-activated protein kinase kinase 1 S218D and S222D mutant
Analyse Structure of the human mitogen-activated protein kinase kinase 1 S218D and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YT3
- Type
- protein
- Length
- 1,205 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase kinase 1, isoform CRA_D
- UniProt
- Q02750
- Ligands
- ANP, MG
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase 1, isoform CRA_D | protein | 297 | 45% helix, 14% strand | Q02750 |
| B | Mitogen-activated protein kinase kinase 1, isoform CRA_D | protein | 311 | 46% helix, 16% strand | Q02750 |
| C | Mitogen-activated protein kinase kinase 1, isoform CRA_D | protein | 288 | 44% helix, 16% strand | Q02750 |
| D | Mitogen-activated protein kinase kinase 1, isoform CRA_D | protein | 309 | 44% helix, 17% strand | Q02750 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.73 | 0.81 | 60 | ANP, MG |
| 2 | 436 | 0.71 | 0.82 | 59 | ANP |
| 3 | 597 | 0.71 | 0.79 | 75 | ANP |
| 4 | 504 | 0.71 | 0.80 | 58 | ANP, MG |
| 5 | 428 | 0.66 | 0.79 | 49 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2016 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1783 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 47 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5YT3 · Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 S218D and S222D mutant · the same entry in another collection · chain D against D, TM-score 1.00
- Q02750 · AlphaFold monomer V2.0 prediction for dual specificity mitogen- activated protein kinase… · a predicted model of the same protein · chain C 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 Q02750
- Elsewhere: RCSB PDB 5YT3 · PDBe 5YT3 · UniProt Q02750
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