Research workbench
2.05 ångström resolution crystal structure of a short chain dehydrogenase from bacillus anthracis str. 'ames ancestor' in complex with NAD+
Analyse 2.05 ångström resolution crystal structure of a short chain dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IJR
- Type
- protein
- Length
- 2,266 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family
- UniProt
- Q81UV8
- Ligands
- NAD, MG, SO4
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, G | Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family | protein | 281 | 43% helix, 14% strand | Q81UV8 |
| B | Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family | protein | 283 | 42% helix, 13% strand | Q81UV8 |
| E | Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family | protein | 280 | 41% helix, 14% strand | Q81UV8 |
| F | Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family | protein | 290 | 39% helix, 13% strand | Q81UV8 |
| H | Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family | protein | 289 | 43% helix, 13% strand | Q81UV8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 14 copies · chains A, D, B, C, H, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.88 | 0.89 | 127 | NAD |
| 2 | 1062 | 0.86 | 0.87 | 117 | NAD |
| 3 | 1064 | 0.86 | 0.87 | 118 | NAD |
| 4 | 1048 | 0.85 | 0.86 | 118 | NAD |
| 5 | 1002 | 0.79 | 0.81 | 99 | SO4 |
Interfaces
16 interfaces between chains.
- C–D · 1997 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 1975 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1972 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 1960 Ų buried · 29 hydrogen bonds · protein-protein
- F–G · 1780 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 modified (engineered).
Compared structures
- 3IJR · 2.05 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus… · 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 Q81UV8
- Elsewhere: RCSB PDB 3IJR · PDBe 3IJR · UniProt Q81UV8
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