Research workbench
A src-like inactive conformation in the abl tyrosine kinase domain
Analyse A src-like inactive conformation in the abl tyrosine kinase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G1T
- Type
- protein
- Length
- 1,130 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase ABL1; ATP-peptide conjugate
- EC
- 2.7.1.112
- UniProt
- P00519
- Ligands
- 112, MG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.1.112) | protein | 271 | 45% helix, 18% strand | P00519 |
| B | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.1.112) | protein | 273 | 43% helix, 18% strand | P00519 |
| C | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.1.112) | protein | 276 | 45% helix, 17% strand | P00519 |
| D | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.1.112) | protein | 277 | 42% helix, 17% strand | P00519 |
| E | ATP-peptide conjugate | protein | 8 | 0% helix, 38% strand | — |
| F | ATP-peptide conjugate | protein | 10 | 0% helix, 40% strand | — |
| G | ATP-peptide conjugate | protein | 7 | 0% helix, 43% strand | — |
| H | ATP-peptide conjugate | protein | 8 | 0% helix, 50% strand | — |
Ligands and binding sites
- 112 · Thiophosphoric acid O-((adenosyl-phospho)phospho)-S-acetamidyl-diester · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.76 | 0.82 | 57 | MG, 112 |
| 2 | 671 | 0.76 | 0.81 | 79 | MG, 112 |
| 3 | 631 | 0.75 | 0.81 | 76 | MG, 112 |
| 4 | 731 | 0.75 | 0.80 | 62 | MG, 112 |
| 5 | 206 | 0.55 | 0.79 | 29 | empty |
Interfaces
8 interfaces between chains.
- A–D · 1179 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 684 Ų buried · 8 hydrogen bonds · protein-protein
- D–H · 671 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 610 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 585 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2G1T · A Src-like Inactive Conformation in the Abl Tyrosine Kinase Domain · the same entry in another collection · chain E against E, TM-score 1.00
- P00519 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ABL1 (P00519) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P00519
- Elsewhere: RCSB PDB 2G1T · PDBe 2G1T · UniProt P00519
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