Research workbench
Crystal structure of braf-V600E bound to GDC0879
Analyse Crystal structure of braf-V600E bound to GDC0879 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MNF
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase B-RAF
- EC
- 2.7.11.1
- UniProt
- P15056
- Ligands
- 29L, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 257 | 40% helix, 17% strand | P15056 |
Ligands and binding sites
- 29L · 2-{4-[(1E)-1-(hydroxyimino)-2,3-dihydro-1H-inden-5-yl]-3-(pyridin-4-yl)-1H-pyrazol-1-yl}ethanol · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.67 | 0.84 | 30 | 29L |
| 2 | 227 | 0.66 | 0.84 | 31 | 29L |
| 3 | 150 | 0.61 | 0.85 | 32 | CL |
| 4 | 172 | 0.55 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1127 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
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 P15056
- Elsewhere: RCSB PDB 4MNF · PDBe 4MNF · UniProt P15056
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