Research workbench
Crystal structure of the rbd domain of SERINE/THREONINE-protein kinase B-RAF from homo sapiens. northeast structural genomics consortium target HR4694F
Analyse Crystal structure of the rbd domain of SERINE/THREONINE-protein kinase B-RAF… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NY5
- Type
- protein
- Length
- 323 residues
- Chains
- 4
- 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
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 80 | 21% helix, 38% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 84 | 20% helix, 38% strand | P15056 |
| C | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 81 | 21% helix, 35% strand | P15056 |
| D | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 78 | 23% helix, 35% strand | P15056 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.62 | 0.80 | 39 | empty |
| 2 | 160 | 0.46 | 0.76 | 27 | empty |
| 3 | 159 | 0.43 | 0.74 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–B · 980 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 564 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 114 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 95 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 65 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3NY5 · Crystal structure of the RBD domain of serine/threonine-protein kinase B-raf from Homo… · the same entry in another collection · chain D against D, TM-score 1.00
- 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 0.92
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 3NY5 · PDBe 3NY5 · UniProt P15056
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