Research workbench
Crystal structure of the small alarmone hydrolase (sah) of pseudomonas aeruginosa
Analyse Crystal structure of the small alarmone hydrolase (sah) of pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YVC
- Type
- protein
- Length
- 695 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional (P)PPGPP SYNTHETASE/GUANOSINE-3',5'- BIS(DIPHOSPHATE) 3'-pyrophosphohydrolase
- UniProt
- A0A071L0I0
- Ligands
- MN
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional (P)PPGPP SYNTHETASE/GUANOSINE-3',5'- BIS(DIPHOSPHATE) 3'-pyrophosphohydrolase | protein | 175 | 71% helix, 2% strand | A0A071L0I0 |
| B | Bifunctional (P)PPGPP SYNTHETASE/GUANOSINE-3',5'- BIS(DIPHOSPHATE) 3'-pyrophosphohydrolase | protein | 173 | 72% helix, 2% strand | A0A071L0I0 |
| C | Bifunctional (P)PPGPP SYNTHETASE/GUANOSINE-3',5'- BIS(DIPHOSPHATE) 3'-pyrophosphohydrolase | protein | 175 | 71% helix, 2% strand | A0A071L0I0 |
| D | Bifunctional (P)PPGPP SYNTHETASE/GUANOSINE-3',5'- BIS(DIPHOSPHATE) 3'-pyrophosphohydrolase | protein | 172 | 73% helix, 2% strand | A0A071L0I0 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.77 | 0.82 | 72 | MN |
| 2 | 517 | 0.69 | 0.79 | 44 | MN |
| 3 | 366 | 0.65 | 0.80 | 37 | MN |
| 4 | 254 | 0.61 | 0.80 | 31 | empty |
| 5 | 196 | 0.52 | 0.78 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1401 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 685 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 292 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 289 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 48 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6YVC · Crystal structure of the small alarmone hydrolase (SAH) of Pseudomonas aeruginosa · 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 A0A071L0I0
- Elsewhere: RCSB PDB 6YVC · PDBe 6YVC · UniProt A0A071L0I0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.