Research workbench
Crystal structure of the bifunctional catalytic fragment of relseq, the RELA/SPOT homolog from streptococcus equisimilis.
Analyse Crystal structure of the bifunctional catalytic fragment of relseq, the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VJ7
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional RELA/SPOT
- EC
- 3.1.7.2, 2.7.6.5
- UniProt
- Q54089
- Ligands
- GDP, GPX, MN
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional RELA/SPOT (EC 3.1.7.2, 2.7.6.5) | protein | 326 | 62% helix, 9% strand | Q54089 |
| B | Bifunctional RELA/SPOT (EC 3.1.7.2, 2.7.6.5) | protein | 310 | 59% helix, 9% strand | Q54089 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- GPX · Guanosine 5'-diphosphate 2':3'-cyclic monophosphate · ligand · chains B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.64 | 0.79 | 45 | GDP |
| 2 | 304 | 0.62 | 0.80 | 39 | GDP |
| 3 | 275 | 0.58 | 0.78 | 29 | GPX |
| 4 | 147 | 0.48 | 0.77 | 18 | empty |
| 5 | 195 | 0.47 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 412 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1VJ7 · Crystal structure of the bifunctional catalytic fragment of RelSeq, the RelA/SpoT homolog… · the same entry in another collection · chain A against A, TM-score 1.00
- Q54089 · AlphaFold monomer V2.0 prediction for bifunctional (P)PPGPP SYNTHASE/HYDROLASE rela… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q54089
- Elsewhere: RCSB PDB 1VJ7 · PDBe 1VJ7 · UniProt Q54089
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