Research workbench
Crystal structure of thermus thermophilus HB8 argininosuccinate synthetase in complex with ATP and citrulline
Analyse Crystal structure of thermus thermophilus HB8 argininosuccinate synthetase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J21
- Type
- protein
- Length
- 1,520 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argininosuccinate synthetase
- EC
- 6.3.4.5
- UniProt
- P59846
- Ligands
- ATP, CIR
- Pockets
- 9 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Argininosuccinate synthetase (EC 6.3.4.5) | protein | 380 | 46% helix, 21% strand | P59846 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- CIR · Citrulline · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.90 | 0.95 | 75 | empty |
| 2 | 1145 | 0.89 | 0.90 | 114 | empty |
| 3 | 1131 | 0.88 | 0.90 | 120 | empty |
| 4 | 841 | 0.77 | 0.80 | 80 | ATP, CIR |
| 5 | 793 | 0.76 | 0.80 | 84 | ATP, CIR |
Interfaces
6 interfaces between chains.
- C–D · 4327 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 4272 Ų buried · 60 hydrogen bonds · protein-protein
- A–D · 1226 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1209 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 905 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1J21 · Crystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- P59846 · AlphaFold monomer V2.0 prediction for argininosuccinate synthase (P59846) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P59846
- Elsewhere: RCSB PDB 1J21 · PDBe 1J21 · UniProt P59846
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