Research workbench
Crystal structure of the 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from thermus thermophilus HB8
Analyse Crystal structure of the 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DFU
- Type
- protein
- Length
- 996 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
- EC
- 5.3.3.10
- UniProt
- Q5SK43
- Pockets
- 16 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (EC 5.3.3.10) | protein | 251 | 16% helix, 41% strand | Q5SK43 |
| B, C | Probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (EC 5.3.3.10) | protein | 249 | 16% helix, 41% strand | Q5SK43 |
| D | Probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (EC 5.3.3.10) | protein | 247 | 14% helix, 42% strand | Q5SK43 |
Pockets
16 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.52 | 0.81 | 29 | empty |
| 2 | 105 | 0.47 | 0.80 | 26 | empty |
| 3 | 112 | 0.45 | 0.78 | 30 | empty |
| 4 | 99 | 0.42 | 0.78 | 21 | empty |
| 5 | 50 | 0.41 | 0.82 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1614 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1572 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 432 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2DFU · Crystal structure of the 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Thermus… · 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 Q5SK43
- Elsewhere: RCSB PDB 2DFU · PDBe 2DFU · UniProt Q5SK43
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