MolNFT v1 · #106259 · protein
Crystal structure of the src tyrosine kinase SH3 domain T96G/Q128R mutant
4RTX · Proto-oncogene tyrosine-protein kinase src: “Crystal structure of the src tyrosine kinase SH3 domain T96G/Q128R mutant”. X-ray diffraction, 2 ligands (NI, SO4), 2 pockets (best druggability 0.65). MolNFT v1 #106259 on GenesisL1: 3D…
- PDB
- 4RTX
- Type
- protein
- Length
- 244 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src
- EC
- 2.7.10.2
- UniProt
- P00523
- Ligands
- NI, SO4
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 61 | 5% helix, 41% strand | P00523 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B, C, D
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 | 511 | 0.65 | 0.77 | 57 | EPE |
| 2 | 581 | 0.65 | 0.76 | 60 | SO4, EPE |
Interfaces
5 interfaces between chains.
- A–C · 373 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 247 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 246 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 158 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 82 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4RTX · Crystal structure of the Src tyrosine kinase SH3 domain T96G/Q128R mutant · the same entry in another collection · chain A against A, 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 P00523
- Elsewhere: RCSB PDB 4RTX · PDBe 4RTX · UniProt P00523
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