MolNFT v2 · #226634 · protein
Crystal structure of CRAF/MEK complex with NST-628 and active RAF dimer
9AYA · RAF proto-oncogene serine/threonine-protein kinase: “Crystal structure of CRAF/MEK complex with NST-628 and active RAF dimer”. X-ray diffraction at 2.59, 3 ligands (A1AHE, ANP, MG), 13 pockets (best druggability 0.85). MolNFT v2…
- PDB
- 9AYA
- Type
- protein
- Length
- 1,123 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.59
- Source
- Homo sapiens
- Molecule
- RAF proto-oncogene serine/threonine-protein kinase; Dual specificity mitogen-activated…
- EC
- 2.7.11.1, 2.7.12.2
- UniProt
- P04049, Q02750
- Ligands
- A1AHE, ANP, MG
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.59 · 4 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAF proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) | protein | 267 | 42% helix, 16% strand | P04049 |
| B | Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 299 | 45% helix, 16% strand | Q02750 |
| C | RAF proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) | protein | 263 | 43% helix, 13% strand | P04049 |
| D | Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 294 | 46% helix, 15% strand | Q02750 |
Ligands and binding sites
- A1AHE · N-[3-fluoro-4-({7-[(3-fluoropyridin-2-yl)oxy]-4-methyl-2-oxo-2H-1-benzopyran-3-yl}methyl)pyridin-2-yl]-N'-methylsulfuric diamide · ligand · 2 copies · chains A, B, C, D
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.85 | 0.86 | 91 | A1AHE, ANP, MG |
| 2 | 645 | 0.78 | 0.83 | 60 | A1AHE, ANP, MG |
| 3 | 898 | 0.75 | 0.79 | 96 | empty |
| 4 | 412 | 0.70 | 0.81 | 45 | empty |
| 5 | 282 | 0.66 | 0.82 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1304 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1137 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 697 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 95 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- Q02750 · AlphaFold monomer V2.0 prediction for dual specificity mitogen- activated protein kinase… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P04049 · AlphaFold monomer V2.0 prediction for RAF proto-oncogene SERINE/THREONINE-protein kinase… · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P04049
- Every structure of UniProt Q02750
- Elsewhere: RCSB PDB 9AYA · PDBe 9AYA · UniProt P04049 · UniProt Q02750
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