MolNFT v1 · #163430 · protein
Structure of the N-terminal catalytic region of T. thermophilus rel bound to ppgpp
6S2T · (P)PPGPP synthetase I, SPOT/RELA: “Structure of the N-terminal catalytic region of T. thermophilus rel bound to ppgpp”. X-ray diffraction, 5 ligands (G4P, MN, MG), 4 pockets (best druggability 0.61). MolNFT v1 #163430 on GenesisL1…
- PDB
- 6S2T
- Type
- protein
- Length
- 350 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (P)PPGPP synthetase I, SPOT/RELA
- EC
- 2.7.6.5
- UniProt
- F6DES6
- Ligands
- G4P, MN, MG, NA, CL
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (P)PPGPP synthetase I, SPOT/RELA (EC 2.7.6.5) | protein | 350 | 58% helix, 11% strand | F6DES6 |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.61 | 0.78 | 39 | GOL, CL |
| 2 | 412 | 0.59 | 0.75 | 48 | G4P, MN, MG |
| 3 | 92 | 0.37 | 0.75 | 16 | empty |
| 4 | 90 | 0.31 | 0.72 | 16 | empty |
Compared structures
- 6S2T · Structure of the N-terminal catalytic region of T. thermophilus Rel bound to ppGpp · 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 F6DES6
- Elsewhere: RCSB PDB 6S2T · PDBe 6S2T · UniProt F6DES6
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