Research workbench
Crystal structure of the abl-SH3 domain complexed with the designed high-affinity peptide ligand P7 at pH 8
Analyse Crystal structure of the abl-SH3 domain complexed with the designed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J9H
- Type
- protein
- Length
- 403 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase ABL1; P7
- EC
- 2.7.10.2
- UniProt
- P00519
- Ligands
- ACE, SO4
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 59 | 5% helix, 49% strand | P00519 |
| B, C, F | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 56 | 5% helix, 52% strand | P00519 |
| D | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 57 | 5% helix, 49% strand | P00519 |
| G, H, I, J, K, L | P7 | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 6 copies · chains A, G, B, H, F, I, E, J, D, K, C, L
- SO4 · Sulfate ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.75 | 0.78 | 93 | empty |
Interfaces
25 interfaces between chains.
- B–H · 503 Ų buried · 4 hydrogen bonds · protein-protein
- C–L · 502 Ų buried · 5 hydrogen bonds · protein-protein
- F–I · 494 Ų buried · 4 hydrogen bonds · protein-protein
- A–G · 494 Ų buried · 6 hydrogen bonds · protein-protein
- D–K · 493 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 4J9H · Crystal structure of the ABL-SH3 domain complexed with the designed high-affinity peptide… · the same entry in another collection · chain L against L, TM-score 1.00
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 4J9H · PDBe 4J9H · UniProt P00519
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