Research workbench
1.99 ångström resolution crystal structure of a short chain dehydrogenase from bacillus anthracis str. 'ames ancestor'
Analyse 1.99 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
- 3IMF
- Type
- protein
- Length
- 986 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short chain dehydrogenase
- UniProt
- Q81MP2
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Short chain dehydrogenase | protein | 248 | 48% helix, 15% strand | Q81MP2 |
| B | Short chain dehydrogenase | protein | 249 | 51% helix, 15% strand | Q81MP2 |
| C | Short chain dehydrogenase | protein | 241 | 50% helix, 15% strand | Q81MP2 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.85 | 0.86 | 56 | ACT |
| 2 | 1118 | 0.80 | 0.81 | 112 | empty |
| 3 | 1077 | 0.76 | 0.78 | 91 | empty |
| 4 | 90 | 0.42 | 0.79 | 20 | empty |
| 5 | 127 | 0.41 | 0.75 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1607 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1601 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1544 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1535 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 636 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 modified (engineered).
Compared structures
- 3IMF · 1.99 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 Q81MP2
- Elsewhere: RCSB PDB 3IMF · PDBe 3IMF · UniProt Q81MP2
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