Research workbench
2.1A crystal structure of GLUCOSE/RIBITOL dehydrogenase from brucella melitensis (P43212)
Analyse 2.1A crystal structure of GLUCOSE/RIBITOL dehydrogenase from brucella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ENN
- Type
- protein
- Length
- 949 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 · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GLUCOSE/RIBITOL dehydrogenase | protein | 238 | 50% helix, 16% strand | Q8YFP3 |
| B | GLUCOSE/RIBITOL dehydrogenase | protein | 242 | 50% helix, 16% strand | Q8YFP3 |
| C | GLUCOSE/RIBITOL dehydrogenase | protein | 235 | 50% helix, 17% strand | Q8YFP3 |
| D | GLUCOSE/RIBITOL dehydrogenase | protein | 234 | 50% helix, 17% strand | Q8YFP3 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.85 | 0.86 | 109 | empty |
| 2 | 276 | 0.54 | 0.76 | 41 | empty |
| 3 | 276 | 0.52 | 0.75 | 35 | empty |
| 4 | 239 | 0.51 | 0.75 | 35 | empty |
| 5 | 233 | 0.48 | 0.74 | 32 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1772 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1769 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1640 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 1633 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 145 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3ENN · 2.1A crystal structure of glucose/ribitol dehydrogenase from brucella melitensis (p43212) · 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 3ENN · PDBe 3ENN · UniProt Q8YFP3
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