Research workbench
Src in complex with DNA-templated macrocyclic inhibitor MC4B
Analyse Src in complex with DNA-templated macrocyclic inhibitor MC4B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U4W
- Type
- protein
- Length
- 277 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src; Macrocyclic inhibitor MC4B
- EC
- 2.7.10.2
- UniProt
- P00523
- Ligands
- FUM, 08M, DAB, SO4
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 275 | 43% helix, 16% strand | P00523 |
| B | Macrocyclic inhibitor MC4B | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- FUM · Fumaric acid · ligand · chains A, B
- 08M · N~5~-(pyrazin-2-ylcarbonyl)-L-ornithine · ligand · chains A, B
- DAB · 2,4-diaminobutyric acid · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.72 | 0.98 | 14 | empty |
| 2 | 196 | 0.54 | 0.79 | 43 | FUM, 08M, DAB |
Interfaces
1 interface between chains.
- A–B · 357 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 3U4W · Src in complex with DNA-templated macrocyclic inhibitor MC4b · the same entry in another collection · chain B against B, TM-score 1.00
- P00523 · AlphaFold monomer V2.0 prediction for proto-oncogene tyrosine-protein kinase src (P00523) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P00523
- Elsewhere: RCSB PDB 3U4W · PDBe 3U4W · UniProt P00523
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