Research workbench
Native structure of a small alarmone hydrolase (relh) from corynebacterium glutamicum
Analyse Native structure of a small alarmone hydrolase (relh) from corynebacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QOD
- Type
- protein
- Length
- 373 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanosine polyphosphate PYROPHOSPHOHYDROLASES/SYNTHETASES
- EC
- 3.1.7.2
- UniProt
- Q8NQV9
- Ligands
- MN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanosine polyphosphate PYROPHOSPHOHYDROLASES/SYNTHETASES (EC 3.1.7.2) | protein | 192 | 72% helix, 1% strand | Q8NQV9 |
| B | Guanosine polyphosphate PYROPHOSPHOHYDROLASES/SYNTHETASES (EC 3.1.7.2) | protein | 181 | 73% helix, 1% strand | Q8NQV9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.67 | 0.76 | 60 | empty |
| 2 | 638 | 0.66 | 0.76 | 53 | PG4 |
| 3 | 79 | 0.34 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1330 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7QOD · Native structure of a small alarmone hydrolase (RelH) from Corynebacterium glutamicum · 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 Q8NQV9
- Elsewhere: RCSB PDB 7QOD · PDBe 7QOD · UniProt Q8NQV9
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