Research workbench
Crystal structure of an oxidoreductase from burkholderia vietnamiensis in complex with NADP
Analyse Crystal structure of an oxidoreductase from burkholderia vietnamiensis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IDY
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- A4JGH3
- Ligands
- NAP, SO4, CL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 262 | 50% helix, 16% strand | A4JGH3 |
| B | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 264 | 49% helix, 16% strand | A4JGH3 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.71 | 0.78 | 65 | NAP |
| 2 | 651 | 0.68 | 0.77 | 60 | SO4, NAP |
| 3 | 464 | 0.63 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1434 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5IDY · Crystal structure of an oxidoreductase from Burkholderia vietnamiensis in complex with… · the same entry in another collection · chain B against B, 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 A4JGH3
- Elsewhere: RCSB PDB 5IDY · PDBe 5IDY · UniProt A4JGH3
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