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Structure of the catalytic domain of T. thermophilus rel in complex with AMP and ppgpp
Analyse Structure of the catalytic domain of T. thermophilus rel in complex with AMP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S2U
- Type
- protein
- Length
- 341 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
- AMP, GN3, TMO, MG, MN
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (P)PPGPP synthetase I, SPOT/RELA (EC 2.7.6.5) | protein | 341 | 58% helix, 12% strand | F6DES6 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- GN3 · [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid · ligand · chains A
- TMO · trimethylamine oxide · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.51 | 0.82 | 19 | empty |
| 2 | 232 | 0.47 | 0.74 | 32 | AMP, GN3, MG |
| 3 | 142 | 0.45 | 0.76 | 23 | empty |
| 4 | 70 | 0.35 | 0.76 | 16 | empty |
Compared structures
- 6S2U · Structure of the catalytic domain of T. thermophilus Rel in complex with AMP and 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 6S2U · PDBe 6S2U · UniProt F6DES6
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