Research workbench
Crystal structure of short chain dehydrogenase reductase sdr glucose-ribitol dehydrogenase from brucella melitensis
Analyse Crystal structure of short chain dehydrogenase reductase sdr glucose-ribitol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GRK
- Type
- protein
- Length
- 1,998 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-(acyl-carrier-protein) reductase (NADH)
- EC
- 1.3.1.9
- UniProt
- Q8YFK8
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Enoyl-(acyl-carrier-protein) reductase (NADH) (EC 1.3.1.9) | protein | 248 | 51% helix, 17% strand | Q8YFK8 |
| B, F, H | Enoyl-(acyl-carrier-protein) reductase (NADH) (EC 1.3.1.9) | protein | 252 | 49% helix, 18% strand | Q8YFK8 |
| D | Enoyl-(acyl-carrier-protein) reductase (NADH) (EC 1.3.1.9) | protein | 251 | 51% helix, 16% strand | Q8YFK8 |
| G | Enoyl-(acyl-carrier-protein) reductase (NADH) (EC 1.3.1.9) | protein | 247 | 52% helix, 17% strand | Q8YFK8 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.86 | 0.87 | 56 | empty |
| 2 | 1071 | 0.86 | 0.87 | 57 | empty |
| 3 | 772 | 0.74 | 0.79 | 46 | empty |
| 4 | 702 | 0.73 | 0.79 | 44 | empty |
| 5 | 744 | 0.73 | 0.78 | 50 | empty |
Interfaces
13 interfaces between chains.
- E–G · 1679 Ų buried · 28 hydrogen bonds · protein-protein
- F–H · 1676 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1675 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1652 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 1519 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3GRK · Crystal structure of short chain dehydrogenase reductase SDR glucose-ribitol… · 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 Q8YFK8
- Elsewhere: RCSB PDB 3GRK · PDBe 3GRK · UniProt Q8YFK8
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