Research workbench
Src in complex with DNA-templated macrocyclic inhibitor MC25B
Analyse Src in complex with DNA-templated macrocyclic inhibitor MC25B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BMM
- Type
- protein
- Length
- 556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src; Macrocyclic inhibitor MC25B
- EC
- 2.7.10.2
- UniProt
- P00523
- Ligands
- FUM, ORN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 275 | 44% helix, 15% strand | P00523 |
| C, D | Macrocyclic inhibitor MC25B | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- FUM · Fumaric acid · ligand · 2 copies · chains A, C, B, D
- ORN · L-ornithine · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.69 | 0.86 | 40 | empty |
| 2 | 277 | 0.54 | 0.76 | 32 | FUM, ORN |
| 3 | 96 | 0.37 | 0.75 | 23 | FUM |
Interfaces
3 interfaces between chains.
- A–B · 592 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 555 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 552 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 4 covalent (nonstandard, covalent ligand).
Compared structures
- 5BMM · Src in complex with DNA-templated macrocyclic inhibitor MC25b · the same entry in another collection · chain A against A, 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 0.94
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 5BMM · PDBe 5BMM · UniProt P00523
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