MolNFT v1 · #188922 · protein
Sfsting with C-di-gmp double fiber
7UN9 · CD-ntase-associated protein 12: “Sfsting with C-di-gmp double fiber”. Electron microscopy, 1 ligand (C2E), 20 pockets (best druggability 0.86). MolNFT v1 #188922 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7UN9
- Type
- protein
- Length
- 2,244 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD-ntase-associated protein 12
- EC
- 3.2.2.5
- UniProt
- A0A2T5Y4G4
- Ligands
- C2E
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | CD-ntase-associated protein 12 (EC 3.2.2.5) | protein | 171 | 38% helix, 23% strand | A0A2T5Y4G4 |
| B, D, J, F, L | CD-ntase-associated protein 12 (EC 3.2.2.5) | protein | 177 | 38% helix, 26% strand | A0A2T5Y4G4 |
| G | CD-ntase-associated protein 12 (EC 3.2.2.5) | protein | 241 | 46% helix, 20% strand | A0A2T5Y4G4 |
| H | CD-ntase-associated protein 12 (EC 3.2.2.5) | protein | 261 | 42% helix, 19% strand | A0A2T5Y4G4 |
| I, K | CD-ntase-associated protein 12 (EC 3.2.2.5) | protein | 172 | 42% helix, 26% strand | A0A2T5Y4G4 |
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 · 6 copies · chains A, B, G, H, C, D, I, J, E, F, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.86 | 0.91 | 57 | empty |
| 2 | 508 | 0.85 | 0.92 | 66 | C2E |
| 3 | 442 | 0.85 | 0.93 | 57 | C2E |
| 4 | 493 | 0.85 | 0.92 | 58 | C2E |
| 5 | 532 | 0.84 | 0.90 | 53 | empty |
Interfaces
24 interfaces between chains.
- G–H · 1765 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1315 Ų buried · 5 hydrogen bonds · protein-protein
- I–J · 1299 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1297 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1278 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7UN9 · SfSTING with c-di-GMP double fiber · 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 A0A2T5Y4G4
- Elsewhere: RCSB PDB 7UN9 · PDBe 7UN9 · UniProt A0A2T5Y4G4
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