MolNFT v1 · #123887 · protein
Crystal structure of a putative short chain dehydrogenase from burkholderia cenocepacia
5JYD: “Crystal structure of a putative short chain dehydrogenase from burkholderia cenocepacia”. X-ray diffraction, 4 ligands (NAD, MG, NA), 20 pockets (best druggability 0.84). MolNFT v1 #123887 on GenesisL1: 3D structure, binding sites…
- PDB
- 5JYD
- Type
- protein
- Length
- 2,330 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short chain dehydrogenase
- UniProt
- B4EEE3
- Ligands
- NAD, MG, NA, IOD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F, G, H | Short chain dehydrogenase | protein | 291 | 43% helix, 13% strand | B4EEE3 |
| B, E | Short chain dehydrogenase | protein | 292 | 44% helix, 13% strand | B4EEE3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H
- IOD · Iodide ion · ion · 54 copies · chains A, G, C, B, D, E, F, H
- EDO · 1,2-ethanediol · additive · 5 copies · chains B, D, E, G, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.84 | 0.86 | 63 | IOD, NA |
| 2 | 860 | 0.83 | 0.85 | 63 | IOD |
| 3 | 800 | 0.82 | 0.85 | 100 | NAD, IOD, EDO |
| 4 | 383 | 0.81 | 0.90 | 56 | NAD, IOD |
| 5 | 433 | 0.80 | 0.88 | 60 | NAD, IOD |
Interfaces
14 interfaces between chains.
- A–B · 2233 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2212 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2193 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 2187 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1655 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5JYD · Crystal Structure of a Putative Short Chain Dehydrogenase from Burkholderia cenocepacia · 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 B4EEE3
- Elsewhere: RCSB PDB 5JYD · PDBe 5JYD · UniProt B4EEE3
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