MolNFT v1 · #12187 · protein
Crystal structure analysis of full-length carboxyl-terminal src kinase at 2.5 a resolution
1K9A: “Crystal structure analysis of full-length carboxyl-terminal src kinase at 2.5 a resolution”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #12187 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1K9A
- Type
- protein
- Length
- 2,627 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxyl-terminal src kinase
- EC
- 2.7.1.112
- UniProt
- P32577
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxyl-terminal src kinase (EC 2.7.1.112) | protein | 439 | 28% helix, 25% strand | P32577 |
| B | Carboxyl-terminal src kinase (EC 2.7.1.112) | protein | 441 | 28% helix, 24% strand | P32577 |
| C | Carboxyl-terminal src kinase (EC 2.7.1.112) | protein | 438 | 30% helix, 23% strand | P32577 |
| D | Carboxyl-terminal src kinase (EC 2.7.1.112) | protein | 433 | 30% helix, 23% strand | P32577 |
| E | Carboxyl-terminal src kinase (EC 2.7.1.112) | protein | 440 | 28% helix, 23% strand | P32577 |
| F | Carboxyl-terminal src kinase (EC 2.7.1.112) | protein | 436 | 27% helix, 23% strand | P32577 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.79 | 0.80 | 109 | empty |
| 2 | 839 | 0.73 | 0.78 | 92 | empty |
| 3 | 953 | 0.73 | 0.77 | 72 | empty |
| 4 | 669 | 0.70 | 0.78 | 76 | empty |
| 5 | 870 | 0.70 | 0.76 | 85 | empty |
Interfaces
6 interfaces between chains.
- B–C · 831 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 749 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 516 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 513 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 346 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1K9A · Crystal structure analysis of full-length carboxyl-terminal Src kinase at 2.5 A resolution · the same entry in another collection · chain F against F, TM-score 1.00
- P32577 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase csk (P32577) · a predicted model of the same protein · chain E against A, TM-score 0.90
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 P32577
- Elsewhere: RCSB PDB 1K9A · PDBe 1K9A · UniProt P32577
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