Research workbench
Crystal structure of thermus thermophilus HB8 argininosuccinate synthetase
Analyse Crystal structure of thermus thermophilus HB8 argininosuccinate synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KH1
- Type
- protein
- Length
- 1,533 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
- SO4
- Pockets
- 10 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argininosuccinate synthetase (EC 6.3.4.5) | protein | 380 | 45% helix, 21% strand | P59846 |
| B | Argininosuccinate synthetase (EC 6.3.4.5) | protein | 382 | 45% helix, 21% strand | P59846 |
| C | Argininosuccinate synthetase (EC 6.3.4.5) | protein | 386 | 46% helix, 21% strand | P59846 |
| D | Argininosuccinate synthetase (EC 6.3.4.5) | protein | 385 | 45% helix, 21% strand | P59846 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.90 | 0.93 | 111 | empty |
| 2 | 1083 | 0.89 | 0.90 | 106 | empty |
| 3 | 1119 | 0.88 | 0.89 | 120 | empty |
| 4 | 787 | 0.77 | 0.81 | 69 | SO4 |
| 5 | 720 | 0.76 | 0.81 | 57 | SO4 |
Interfaces
6 interfaces between chains.
- C–D · 4776 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 4411 Ų buried · 55 hydrogen bonds · protein-protein
- A–D · 1243 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1202 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 963 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1KH1 · Crystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase · 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 1KH1 · PDBe 1KH1 · UniProt P59846
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