Research workbench
Gasdermin-B C-terminal domain containing the polymorphism residues GLY299:SER306 fused to maltose binding protein
Analyse Gasdermin-B C-terminal domain containing the polymorphism residues… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TJ2
- Type
- protein
- Length
- 2,127 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein
- UniProt
- A0A178SBV6, Q8TAX9
- Ligands
- GLC
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein | protein | 534 | 55% helix, 15% strand | A0A178SBV6, Q8TAX9 |
| B | Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein | protein | 536 | 55% helix, 15% strand | A0A178SBV6, Q8TAX9 |
| C | Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein | protein | 529 | 54% helix, 16% strand | A0A178SBV6, Q8TAX9 |
| D | Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein | protein | 528 | 54% helix, 15% strand | A0A178SBV6, Q8TAX9 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.72 | 0.85 | 29 | GLC |
| 2 | 253 | 0.71 | 0.86 | 26 | GLC |
| 3 | 290 | 0.70 | 0.84 | 31 | GLC |
| 4 | 107 | 0.70 | 0.92 | 22 | empty |
| 5 | 513 | 0.70 | 0.80 | 64 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1253 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 673 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 457 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5TJ2 · Gasdermin-B C-terminal domain containing the polymorphism residues Gly299:Ser306 fused to… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8TAX9 · AlphaFold monomer V2.0 prediction for gasdermin-B (Q8TAX9) · a predicted model of the same protein · chain B against A, TM-score 0.33
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 A0A178SBV6
- Every structure of UniProt Q8TAX9
- Elsewhere: RCSB PDB 5TJ2 · PDBe 5TJ2 · UniProt A0A178SBV6 · UniProt Q8TAX9
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