Research workbench
Deoxyguanylosuccinate synthase (dgss) quaternary structure with amppcp, dgmp, asp, magnesium at 2.21 ångström resolution
Analyse Deoxyguanylosuccinate synthase (dgss) quaternary structure with amppcp, dgmp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TNH
- Type
- protein
- Length
- 689 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylosuccinate synthetase
- UniProt
- G3FFN6
- Ligands
- DGP, ACP, ASP, MG, SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylosuccinate synthetase | protein | 345 | 35% helix, 20% strand | G3FFN6 |
| B | Adenylosuccinate synthetase | protein | 344 | 35% helix, 20% strand | G3FFN6 |
Ligands and binding sites
- DGP · 2'-deoxyguanosine-5'-monophosphate · ligand · 2 copies · chains A, B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- ASP · Aspartic acid · ligand · chains A
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.78 | 0.98 | 31 | empty |
| 2 | 521 | 0.78 | 0.85 | 61 | DGP, ACP, ASP |
| 3 | 362 | 0.78 | 0.88 | 51 | DGP, ACP, MG |
| 4 | 237 | 0.50 | 0.75 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 2586 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6TNH · Deoxyguanylosuccinate synthase (DgsS) quaternary structure with AMPPcP, dGMP, Asp… · 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 G3FFN6
- Elsewhere: RCSB PDB 6TNH · PDBe 6TNH · UniProt G3FFN6
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