MolNFT v1 · #177219 · protein
Bacterial sting in complex with C-di-gmp
7EBD · Tir-like domain-containing protein: “Bacterial sting in complex with C-di-gmp”. X-ray diffraction, 1 ligand (C2E), 4 pockets (best druggability 0.84). MolNFT v1 #177219 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7EBD
- Type
- protein
- Length
- 316 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tir-like domain-containing protein
- UniProt
- A0A133PTK7
- Ligands
- C2E
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tir-like domain-containing protein | protein | 158 | 47% helix, 20% strand | A0A133PTK7 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.84 | 0.90 | 68 | C2E |
| 2 | 83 | 0.38 | 0.77 | 17 | empty |
| 3 | 53 | 0.31 | 0.76 | 16 | empty |
| 4 | 50 | 0.28 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1179 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 7EBD · Bacterial STING in complex with c-di-GMP · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A133PTK7
- Elsewhere: RCSB PDB 7EBD · PDBe 7EBD · UniProt A0A133PTK7
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