Research workbench
Crystal structure of the sorghum bicolor dhurrinase 1
Analyse Crystal structure of the sorghum bicolor dhurrinase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V02
- Type
- protein
- Length
- 2,904 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dhurrinase
- EC
- 3.2.1.21
- UniProt
- Q41290
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Dhurrinase (EC 3.2.1.21) | protein | 484 | 44% helix, 17% strand | Q41290 |
| E | Dhurrinase (EC 3.2.1.21) | protein | 484 | 45% helix, 17% strand | Q41290 |
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.73 | 0.76 | 100 | empty |
| 2 | 376 | 0.72 | 0.83 | 53 | empty |
| 3 | 352 | 0.71 | 0.83 | 45 | empty |
| 4 | 442 | 0.71 | 0.81 | 58 | empty |
| 5 | 637 | 0.70 | 0.78 | 68 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1085 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1070 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1064 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 520 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 351 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1V02 · Crystal structure of the Sorghum bicolor dhurrinase 1 · 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 Q41290
- Elsewhere: RCSB PDB 1V02 · PDBe 1V02 · UniProt Q41290
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