Research workbench
Crystal structure of a short-chain dehydrogenase/reductase superfamily protein from agrobacterium tumefaciens (TARGET EFI-506441) with bound NAD, monoclinic form 2
Analyse Crystal structure of a short-chain dehydrogenase/reductase superfamily protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IDG
- Type
- protein
- Length
- 656 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Agrobacterium fabrum
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE
- UniProt
- A9CL58
- Ligands
- NAD, CL
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.9 · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Short-chain DEHYDROGENASE/REDUCTASE | protein | 328 | 45% helix, 19% strand | A9CL58 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.78 | 0.80 | 67 | CL, NAD, EDO |
| 2 | 932 | 0.77 | 0.79 | 65 | NAD, CL |
| 3 | 72 | 0.48 | 0.83 | 16 | empty |
| 4 | 192 | 0.44 | 0.74 | 33 | empty |
| 5 | 95 | 0.37 | 0.76 | 19 | EDO |
Interfaces
1 interface between chains.
- A–B · 880 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4IDG · Crystal structure of a short-chain DEHYDROGENASE/REDUCTASE superfamily protein from… · 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 A9CL58
- Elsewhere: RCSB PDB 4IDG · PDBe 4IDG · UniProt A9CL58
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