MolNFT v1 · #169391 · protein
Apo braf dimer bound to 14-3-3
6XAG · 14-3-3 protein ZETA/DELTA: “Apo braf dimer bound to 14-3-3”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #169391 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XAG
- Type
- protein
- Length
- 1,007 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein ZETA/DELTA; SERINE/THREONINE-protein kinase B-RAF
- EC
- 2.7.11.1
- UniProt
- P63104, P15056
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein ZETA/DELTA | protein | 230 | 83% helix, 0% strand | P63104 |
| B | 14-3-3 protein ZETA/DELTA | protein | 223 | 81% helix, 0% strand | P63104 |
| C | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 276 | 37% helix, 16% strand | P15056 |
| D | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 278 | 37% helix, 15% strand | P15056 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.82 | 0.86 | 67 | empty |
| 2 | 595 | 0.69 | 0.78 | 60 | empty |
| 3 | 230 | 0.65 | 0.83 | 25 | empty |
| 4 | 234 | 0.59 | 0.80 | 26 | empty |
| 5 | 52 | 0.58 | 0.92 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1252 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1094 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 842 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 717 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 676 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6XAG · Apo BRAF dimer bound to 14-3-3 · the same entry in another collection · chain D against D, TM-score 1.00
- P63104 · AlphaFold monomer V2.0 prediction for 14-3-3 protein ZETA/DELTA (P63104) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P15056 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase B-RAF (P15056) · a predicted model of the same protein · chain D against A, TM-score 0.91
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 P63104
- Every structure of UniProt P15056
- Elsewhere: RCSB PDB 6XAG · PDBe 6XAG · UniProt P63104 · UniProt P15056
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