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The crystal structure of adenylosuccinate lyase from pyrobaculum aerophilum: insights into thermal stability and human pathology
Analyse The crystal structure of adenylosuccinate lyase from pyrobaculum aerophilum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DOF
- Type
- protein
- Length
- 1,540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylosuccinate lyase
- EC
- 4.3.2.2
- UniProt
- Q8ZY28
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Adenylosuccinate lyase (EC 4.3.2.2) | protein | 385 | 66% helix, 5% strand | Q8ZY28 |
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.79 | 0.98 | 22 | empty |
| 2 | 114 | 0.79 | 0.98 | 20 | empty |
| 3 | 809 | 0.76 | 0.80 | 67 | empty |
| 4 | 782 | 0.76 | 0.80 | 62 | empty |
| 5 | 837 | 0.75 | 0.79 | 66 | empty |
Interfaces
6 interfaces between chains.
- C–D · 4512 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 4504 Ų buried · 45 hydrogen bonds · protein-protein
- A–D · 2063 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 2051 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 1040 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1DOF · The crystal structure of adenylosuccinate lyase from pyrobaculum aerophilum: insights… · the same entry in another collection · chain D against D, 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 Q8ZY28
- Elsewhere: RCSB PDB 1DOF · PDBe 1DOF · UniProt Q8ZY28
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