Research workbench
Crystal structure of the pleckstrin-homology domain of BCR-abl in complex with monobody MB(BCR-PH_4).
Analyse Crystal structure of the pleckstrin-homology domain of BCR-abl in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OC7
- Type
- protein
- Length
- 404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Breakpoint cluster region PROTEIN,PLECKSTRIN-homology domain of BCR-abl; Monobody…
- EC
- 2.7.11.1
- UniProt
- P11274
- Ligands
- IP2
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Breakpoint cluster region PROTEIN,PLECKSTRIN-homology domain of BCR-abl (EC 2.7.11.1) | protein | 112 | 25% helix, 47% strand | P11274 |
| A | Breakpoint cluster region PROTEIN,PLECKSTRIN-homology domain of BCR-abl (EC 2.7.11.1) | protein | 111 | 25% helix, 46% strand | P11274 |
| C | Monobody MB(BCR-PH_4) | protein | 92 | 0% helix, 57% strand | — |
| B | Monobody MB(BCR-PH_4) | protein | 89 | 0% helix, 58% strand | — |
Ligands and binding sites
- IP2 · D-myo-inositol-4,5-bisphosphate · ligand · chains D
- GOL · Glycerol · additive · 7 copies · chains D, A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.48 | 0.78 | 15 | empty |
| 2 | 76 | 0.45 | 0.81 | 17 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 518 Ų buried · 8 hydrogen bonds · protein-protein
- D–A · 498 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 159 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5OC7 · Crystal structure of the pleckstrin-homology domain of Bcr-Abl in complex with monobody… · the same entry in another collection · chain D against D, TM-score 1.00
- P11274 · AlphaFold monomer V2.0 prediction for breakpoint cluster region protein (P11274) · a predicted model of the same protein · chain A 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 P11274
- Elsewhere: RCSB PDB 5OC7 · PDBe 5OC7 · UniProt P11274
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