Research workbench
C-src in complex with ATP-chf
Analyse C-src in complex with ATP-chf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XP5
- Type
- protein
- Length
- 534 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
- 8BU, MG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 267 | 40% helix, 16% strand | P00523 |
Ligands and binding sites
- 8BU · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl) oxolan-2-yl]methoxy-[(S)-fluoranyl-[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.69 | 0.76 | 66 | 8BU, MG |
| 2 | 451 | 0.67 | 0.79 | 48 | 8BU, MG |
| 3 | 303 | 0.59 | 0.78 | 35 | empty |
| 4 | 96 | 0.34 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 402 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5XP5 · C-Src in complex with ATP-Chf · 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 5XP5 · PDBe 5XP5 · UniProt P00523
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