MolNFT v1 · #139756 · protein
C-src in complex with ATP-chcl
5XP7 · Proto-oncogene tyrosine-protein kinase src: “C-src in complex with ATP-chcl”. X-ray diffraction, 2 ligands (8C6, MG), 2 pockets (best druggability 0.76). MolNFT v1 #139756 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5XP7
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- 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
- 8C6, MG
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 265 | 41% helix, 17% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 267 | 41% helix, 18% strand | P00523 |
Ligands and binding sites
- 8C6 · [(R)-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]-chloranyl-methyl]phosphonic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
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 | 1197 | 0.76 | 0.78 | 112 | 8C6, MG, GOL |
| 2 | 309 | 0.59 | 0.77 | 38 | 8C6 |
Interfaces
1 interface between chains.
- A–B · 416 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5XP7 · C-Src in complex with ATP-CHCl · 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 5XP7 · PDBe 5XP7 · UniProt P00523
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