Research workbench
Crystal structure of a short chain DEHYDROGENASE/REDUCTASE sdr from burkholderia phymatum in complex with NAD
Analyse Crystal structure of a short chain DEHYDROGENASE/REDUCTASE sdr from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IG2
- Type
- protein
- Length
- 838 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- B2JGP2
- Ligands
- NAD
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 278 | 55% helix, 12% strand | B2JGP2 |
| B | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 281 | 54% helix, 12% strand | B2JGP2 |
| C | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 279 | 55% helix, 12% strand | B2JGP2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.81 | 0.85 | 90 | NAD, ACT |
| 2 | 378 | 0.80 | 0.89 | 60 | NAD, ACT |
| 3 | 725 | 0.79 | 0.83 | 106 | NAD, ACT |
| 4 | 381 | 0.61 | 0.77 | 57 | empty |
| 5 | 121 | 0.48 | 0.80 | 23 | empty |
Interfaces
2 interfaces between chains.
- B–C · 2716 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 440 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5IG2 · Crystal structure of a short chain dehydrogenase/reductase SDR from Burkholderia phymatum… · 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 B2JGP2
- Elsewhere: RCSB PDB 5IG2 · PDBe 5IG2 · UniProt B2JGP2
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