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The crystal structure of a hyperthermoactive exopolygalacturonase from thermotoga maritima
Analyse The crystal structure of a hyperthermoactive exopolygalacturonase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JUR
- Type
- protein
- Length
- 1,778 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-poly-alpha-D-galacturonosidase
- EC
- 3.2.1.15
- UniProt
- Q9WYR8
- Pockets
- 13 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Exo-poly-alpha-D-galacturonosidase (EC 3.2.1.15) | protein | 444 | 15% helix, 48% strand | Q9WYR8 |
| D | Exo-poly-alpha-D-galacturonosidase (EC 3.2.1.15) | protein | 446 | 15% helix, 47% strand | Q9WYR8 |
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.58 | 0.74 | 62 | empty |
| 2 | 401 | 0.56 | 0.74 | 54 | empty |
| 3 | 322 | 0.56 | 0.76 | 44 | empty |
| 4 | 151 | 0.45 | 0.77 | 31 | empty |
| 5 | 135 | 0.44 | 0.77 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–D · 759 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 752 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 752 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 751 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3JUR · The crystal structure of a hyperthermoactive Exopolygalacturonase from Thermotoga maritima · the same entry in another collection · 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 Q9WYR8
- Elsewhere: RCSB PDB 3JUR · PDBe 3JUR · UniProt Q9WYR8
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