MolNFT v1 · #124193 · protein
Fully ligated adenylosuccinate synthetase from pyrococcus horikoshii OT3 with GTP, imp and hadacidin
5K7X: “Fully ligated adenylosuccinate synthetase from pyrococcus horikoshii OT3 with GTP, imp and hadacidin”. X-ray diffraction, 4 ligands (GTP, IMP, HDA), 18 pockets (best druggability 0.89). MolNFT v1 #124193 on GenesisL1: 3D structure…
- PDB
- 5K7X
- Type
- protein
- Length
- 2,022 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylosuccinate synthetase
- EC
- 6.3.4.4
- UniProt
- O58187
- Ligands
- GTP, IMP, HDA, MG
- Pockets
- 18 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Adenylosuccinate synthetase (EC 6.3.4.4) | protein | 337 | 36% helix, 20% strand | O58187 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- IMP · Inosinic acid · ligand · 6 copies · chains A, B, C, D, E, F
- HDA · Hadacidin · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.89 | 0.93 | 108 | GTP, IMP, HDA |
| 2 | 121 | 0.80 | 0.99 | 27 | empty |
| 3 | 444 | 0.80 | 0.88 | 63 | GTP, IMP, HDA |
| 4 | 115 | 0.80 | 0.99 | 22 | empty |
| 5 | 114 | 0.80 | 0.99 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2374 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2372 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2332 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 688 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 189 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5K7X · Fully ligated Adenylosuccinate Synthetase from Pyrococcus horikoshii OT3 with GTP, IMP… · the same entry in another collection · chain C against C, TM-score 1.00
- O58187 · AlphaFold monomer V2.0 prediction for adenylosuccinate synthetase (O58187) · a predicted model of the same protein · 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 O58187
- Elsewhere: RCSB PDB 5K7X · PDBe 5K7X · UniProt O58187
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.