Research workbench
Crystal structure of the abl-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions
Analyse Crystal structure of the abl-SH3 domain complexed with a designed high-affinity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BBZ
- Type
- protein
- Length
- 272 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abl tyrosine kinase; Peptide P41
- UniProt
- P00519
- Ligands
- ACE, SO4
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Abl tyrosine kinase | protein | 58 | 5% helix, 50% strand | P00519 |
| B, D, F, H | Peptide P41 | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D, E, F, G, H
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 | 109 | 0.41 | 0.76 | 23 | empty |
| 2 | 96 | 0.35 | 0.74 | 22 | empty |
Interfaces
10 interfaces between chains.
- G–H · 507 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 498 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 495 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 490 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 335 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1BBZ · Crystal structure of the abl-SH3 domain complexed with a designed high-affinity peptide… · the same entry in another collection · chain H against H, TM-score 1.00
- P00519 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ABL1 (P00519) · a predicted model of the same protein · chain E against A, TM-score 0.95
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 1BBZ · PDBe 1BBZ · UniProt P00519
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.