Research workbench
Gasdermin-B C-terminal domain containing the polymorphism residues ARG299: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
- 5TIB
- Type
- protein
- Length
- 1,063 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN- B
- UniProt
- A0A178SBV6, Q8TAX9
- Ligands
- GLC, NA
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN- B | protein | 533 | 53% helix, 15% strand | A0A178SBV6, Q8TAX9 |
| B | Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN- B | protein | 530 | 53% helix, 15% strand | A0A178SBV6, Q8TAX9 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- NA · Sodium ion · metal · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.72 | 0.85 | 35 | GLC |
| 2 | 257 | 0.70 | 0.85 | 28 | GLC |
| 3 | 301 | 0.65 | 0.81 | 56 | empty |
| 4 | 297 | 0.64 | 0.81 | 41 | empty |
| 5 | 155 | 0.64 | 0.86 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1351 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5TIB · Gasdermin-B C-terminal domain containing the polymorphism residues Arg299:Ser306 fused to… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TAX9 · AlphaFold monomer V2.0 prediction for gasdermin-B (Q8TAX9) · a predicted model of the same protein · chain A against A, TM-score 0.32
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 5TIB · PDBe 5TIB · UniProt A0A178SBV6 · UniProt Q8TAX9
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