Research workbench
Crystal structure of lck SH2-SH3 with SH2 binding site of P130CAS
Analyse Crystal structure of lck SH2-SH3 with SH2 binding site of P130CAS in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X27
- Type
- protein
- Length
- 1,013 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase lck; Crk-associated substrate
- EC
- 2.7.1.112
- UniProt
- P06239, Q63767
- Ligands
- NA
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | Proto-oncogene tyrosine-protein kinase lck (EC 2.7.1.112) | protein | 163 | 12% helix, 39% strand | P06239 |
| B, C | Proto-oncogene tyrosine-protein kinase lck (EC 2.7.1.112) | protein | 164 | 13% helix, 38% strand | P06239 |
| I | Crk-associated substrate | protein | 5 | 0% helix, 0% strand | Q63767 |
| J, L, N | Crk-associated substrate | protein | 6 | 0% helix, 0% strand | Q63767 |
| K, M | Crk-associated substrate | protein | 5 | 0% helix, 0% strand | Q63767 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.78 | 0.80 | 89 | empty |
| 2 | 898 | 0.74 | 0.78 | 71 | empty |
| 3 | 673 | 0.68 | 0.76 | 50 | empty |
| 4 | 100 | 0.67 | 0.91 | 32 | empty |
| 5 | 677 | 0.66 | 0.75 | 45 | empty |
Interfaces
30 interfaces between chains.
- A–F · 1019 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1012 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 977 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 906 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 890 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
- 1X27 · Crystal Structure of Lck SH2-SH3 with SH2 binding site of p130Cas · the same entry in another collection · chain N against N, 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 P06239
- Every structure of UniProt Q63767
- Elsewhere: RCSB PDB 1X27 · PDBe 1X27 · UniProt P06239 · UniProt Q63767
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