Research workbench
Crystal structure of putative short-chain DEHYDROGENASE/REDUCTASE from burkholderia xenovorans LB400 bound to NAD
Analyse Crystal structure of putative short-chain DEHYDROGENASE/REDUCTASE from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JY1
- Type
- protein
- Length
- 1,064 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative short-chain DEHYDROGENASE/REDUCTASE
- EC
- 1.1.1.100
- UniProt
- Q13HF0
- Ligands
- NAD, CL
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative short-chain DEHYDROGENASE/REDUCTASE (EC 1.1.1.100) | protein | 266 | 50% helix, 15% strand | Q13HF0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.84 | 0.85 | 72 | EDO |
| 2 | 760 | 0.76 | 0.80 | 71 | NAD, CL, EDO, ACT |
| 3 | 698 | 0.76 | 0.81 | 63 | NAD, CL, EDO, ACT |
| 4 | 711 | 0.75 | 0.81 | 63 | NAD, ACT, CL, EDO |
| 5 | 693 | 0.75 | 0.81 | 56 | NAD, EDO, ACT, CL |
Interfaces
6 interfaces between chains.
- A–C · 2172 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 2166 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1544 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1533 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 701 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5JY1 · Crystal Structure of putative short-chain dehydrogenase/reductase from Burkholderia… · 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 Q13HF0
- Elsewhere: RCSB PDB 5JY1 · PDBe 5JY1 · UniProt Q13HF0
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