Research workbench
Crystal structure of D-psicose 3-epimerase (dpease) in the absence of substrate
Analyse Crystal structure of D-psicose 3-epimerase (dpease) in the absence of substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HK0
- Type
- protein
- Length
- 1,156 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-psicose 3-epimerase
- EC
- 5.3.1.-
- UniProt
- Q8U6Q7
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-psicose 3-epimerase (EC 5.3.1.-) | protein | 289 | 47% helix, 14% strand | Q8U6Q7 |
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.87 | 0.90 | 85 | empty |
| 2 | 1032 | 0.84 | 0.84 | 99 | empty |
| 3 | 1053 | 0.83 | 0.84 | 88 | empty |
| 4 | 99 | 0.44 | 0.79 | 18 | empty |
| 5 | 153 | 0.42 | 0.74 | 34 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1410 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 1402 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 484 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 483 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 311 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 2HK0 · Crystal structure of D-psicose 3-epimerase (DPEase) in the absence of substrate · 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 Q8U6Q7
- Elsewhere: RCSB PDB 2HK0 · PDBe 2HK0 · UniProt Q8U6Q7
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