Research workbench
Crystal structure of a short-chain DEHYDROGENASE/REDUCTASE superfamily protein from agrobacterium tumefaciens (target efi-506441) with bound NAD, monoclinic form 1
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
- 4ID9
- Type
- protein
- Length
- 649 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE
- UniProt
- A9CL58
- Ligands
- NAD, ALA, CL
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain DEHYDROGENASE/REDUCTASE | protein | 321 | 45% helix, 19% strand | A9CL58 |
| B | Short-chain DEHYDROGENASE/REDUCTASE | protein | 328 | 45% helix, 18% strand | A9CL58 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ALA · Alanine · ligand · chains A
- CL · Chloride ion · ion · 2 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 | 1004 | 0.78 | 0.80 | 67 | CL, NAD |
| 2 | 1005 | 0.77 | 0.79 | 62 | CL, NAD |
| 3 | 87 | 0.43 | 0.79 | 22 | empty |
| 4 | 162 | 0.42 | 0.74 | 32 | empty |
| 5 | 94 | 0.38 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 912 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4ID9 · 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 4ID9 · PDBe 4ID9 · UniProt A9CL58
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