Research workbench
2.5A crystal structure of GLUCOSE/RIBITOL dehydrogenase from brucella melitensis
Analyse 2.5A crystal structure of GLUCOSE/RIBITOL dehydrogenase from brucella melitensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EMK
- Type
- protein
- Length
- 947 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLUCOSE/RIBITOL dehydrogenase
- UniProt
- Q8YFP3
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GLUCOSE/RIBITOL dehydrogenase | protein | 241 | 49% helix, 16% strand | Q8YFP3 |
| B | GLUCOSE/RIBITOL dehydrogenase | protein | 232 | 48% helix, 16% strand | Q8YFP3 |
| C | GLUCOSE/RIBITOL dehydrogenase | protein | 236 | 50% helix, 16% strand | Q8YFP3 |
| D | GLUCOSE/RIBITOL dehydrogenase | protein | 238 | 50% helix, 16% strand | Q8YFP3 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.85 | 0.86 | 115 | empty |
| 2 | 380 | 0.60 | 0.77 | 41 | empty |
| 3 | 260 | 0.52 | 0.75 | 36 | empty |
| 4 | 199 | 0.49 | 0.76 | 33 | empty |
| 5 | 78 | 0.43 | 0.80 | 24 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1839 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1833 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1660 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1658 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 138 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3EMK · 2.5A crystal structure of glucose/ribitol dehydrogenase from brucella melitensis · 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 Q8YFP3
- Elsewhere: RCSB PDB 3EMK · PDBe 3EMK · UniProt Q8YFP3
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