Research workbench
Crystal structure of adenylosuccinate synthetase (ampsase) (pura) from burkholderia thailandensis
Analyse Crystal structure of adenylosuccinate synthetase (ampsase) (pura) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UE9
- Type
- protein
- Length
- 1,696 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylosuccinate synthetase
- EC
- 6.3.4.4
- UniProt
- Q2SWD3
- Ligands
- NA, CA
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylosuccinate synthetase (EC 6.3.4.4) | protein | 424 | 38% helix, 21% strand | Q2SWD3 |
| B | Adenylosuccinate synthetase (EC 6.3.4.4) | protein | 421 | 38% helix, 22% strand | Q2SWD3 |
| C | Adenylosuccinate synthetase (EC 6.3.4.4) | protein | 426 | 37% helix, 21% strand | Q2SWD3 |
| D | Adenylosuccinate synthetase (EC 6.3.4.4) | protein | 425 | 37% helix, 21% strand | Q2SWD3 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains C, D
- ACT · Acetate ion · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.85 | 0.97 | 32 | empty |
| 2 | 236 | 0.85 | 0.97 | 35 | empty |
| 3 | 821 | 0.77 | 0.81 | 102 | ACT |
| 4 | 742 | 0.73 | 0.79 | 84 | empty |
| 5 | 723 | 0.69 | 0.77 | 77 | empty |
Interfaces
4 interfaces between chains.
- B–D · 2673 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 2665 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 385 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 88 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3UE9 · Crystal structure of Adenylosuccinate synthetase (AMPSase) (purA) from Burkholderia… · the same entry in another collection · chain D against D, TM-score 1.00
- Q2SWD3 · AlphaFold monomer V2.0 prediction for adenylosuccinate synthetase (Q2SWD3) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q2SWD3
- Elsewhere: RCSB PDB 3UE9 · PDBe 3UE9 · UniProt Q2SWD3
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