MolNFT v1 · #135207 · protein
Crystal structure of a 3-oxoacyl-[acyl-carrier protein] reductase with bound NAD from brucella melitensis
5TS3 · Short-chain DEHYDROGENASE/REDUCTASE sdr: “Crystal structure of a 3-oxoacyl-[acyl-carrier protein] reductase with bound NAD from brucella melitensis”. X-ray diffraction, 1 ligand (NAD), 6 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 5TS3
- Type
- protein
- Length
- 527 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- C0RKU3
- Ligands
- NAD
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 265 | 47% helix, 15% strand | C0RKU3 |
| B | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 262 | 46% helix, 15% strand | C0RKU3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
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 | 484 | 0.75 | 0.83 | 45 | NAD, EDO |
| 2 | 416 | 0.70 | 0.82 | 41 | NAD, EDO |
| 3 | 151 | 0.48 | 0.78 | 31 | empty |
| 4 | 85 | 0.39 | 0.77 | 15 | empty |
| 5 | 74 | 0.38 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1809 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5TS3 · Crystal Structure of a 3-oxoacyl-[acyl-carrier protein] Reductase with bound NAD 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 C0RKU3
- Elsewhere: RCSB PDB 5TS3 · PDBe 5TS3 · UniProt C0RKU3
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