Research workbench
3D domain-swapped dimer of the maltose-binding protein fused to a fragment of the protein-tyrosine kinase 2-beta
Analyse 3D domain-swapped dimer of the maltose-binding protein fused to a fragment of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LF3
- Type
- protein
- Length
- 2,210 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,PROTEIN- tyrosine kinase 2-beta
- EC
- 2.7.10.2
- UniProt
- P0AEX9, Q14289
- Ligands
- GLC
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,PROTEIN- tyrosine kinase 2-beta (EC 2.7.10.2) | protein | 369 | 46% helix, 21% strand | P0AEX9, Q14289 |
| C, D, E, F | MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,PROTEIN- tyrosine kinase 2-beta (EC 2.7.10.2) | protein | 368 | 46% helix, 21% strand | P0AEX9, Q14289 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 309 | 0.75 | 0.87 | 30 | GLC |
| 2 | 248 | 0.73 | 0.87 | 27 | GLC |
| 3 | 287 | 0.73 | 0.86 | 30 | GLC |
| 4 | 258 | 0.72 | 0.86 | 28 | GLC |
| 5 | 259 | 0.72 | 0.86 | 27 | GLC |
Interfaces
11 interfaces between chains.
- A–B · 11749 Ų buried · 199 hydrogen bonds · protein-protein
- E–F · 11710 Ų buried · 196 hydrogen bonds · protein-protein
- C–D · 11627 Ų buried · 205 hydrogen bonds · protein-protein
- B–E · 258 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 243 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6LF3 · 3D domain-swapped dimer of the maltose-binding protein fused to a fragment of the… · the same entry in another collection · chain F against F, TM-score 1.00
- Q14289 · AlphaFold monomer V2.0 prediction for protein-tyrosine kinase 2-beta (Q14289) · a predicted model of the same protein · chain F against A, TM-score 0.31
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 P0AEX9
- Every structure of UniProt Q14289
- Elsewhere: RCSB PDB 6LF3 · PDBe 6LF3 · UniProt P0AEX9 · UniProt Q14289
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