MolNFT v1 · #121699 · protein
Adenylosuccinate synthetase from cryptococcus neoformans complexed with GDP and imp
5I34: “Adenylosuccinate synthetase from cryptococcus neoformans complexed with GDP and imp”. X-ray diffraction, 2 ligands (GDP, IMP), 8 pockets (best druggability 0.85). MolNFT v1 #121699 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5I34
- Type
- protein
- Length
- 842 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylosuccinate synthetase
- EC
- 6.3.4.4
- UniProt
- J9VI09
- Ligands
- GDP, IMP
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylosuccinate synthetase (EC 6.3.4.4) | protein | 429 | 38% helix, 22% strand | J9VI09 |
| B | Adenylosuccinate synthetase (EC 6.3.4.4) | protein | 413 | 39% helix, 21% strand | J9VI09 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- IMP · Inosinic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.85 | 0.98 | 31 | empty |
| 2 | 728 | 0.79 | 0.83 | 81 | empty |
| 3 | 584 | 0.78 | 0.84 | 69 | GDP, IMP |
| 4 | 546 | 0.72 | 0.81 | 64 | GDP, IMP |
| 5 | 110 | 0.38 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2811 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 5I34 · Adenylosuccinate synthetase from Cryptococcus neoformans complexed with GDP and IMP · 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 J9VI09
- Elsewhere: RCSB PDB 5I34 · PDBe 5I34 · UniProt J9VI09
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