Research workbench
Crystal structure of the abl-SH3 domain complexed with the high affinity peptide P0
Analyse Crystal structure of the abl-SH3 domain complexed with the high affinity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J9F
- Type
- protein
- Length
- 209 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase ABL1; P0
- EC
- 2.7.10.2
- UniProt
- P00519
- Ligands
- ACE, SO4
- Pockets
- 1 · best druggability 0.41
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 62 | 5% helix, 48% strand | P00519 |
| B, D, F | P0 | protein | 10 | 0% helix, 0% strand | — |
| C | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 57 | 5% helix, 49% strand | P00519 |
| E | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 60 | 5% helix, 48% strand | P00519 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · chains A, E
- GOL · Glycerol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.41 | 0.73 | 21 | empty |
Interfaces
8 interfaces between chains.
- C–D · 507 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 495 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 484 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 403 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4J9F · Crystal structure of the Abl-SH3 domain complexed with the high affinity peptide P0 · the same entry in another collection · chain F against F, TM-score 1.00
- P00519 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ABL1 (P00519) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P00519
- Elsewhere: RCSB PDB 4J9F · PDBe 4J9F · UniProt P00519
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