MolNFT v1 · #92869 · protein
Crystal structure of a short chain dehydrogenase homolog (target efi- 505321) from burkholderia multivorans, with bound NAD
4GLO · 3-oxoacyl-[acyl-carrier protein] reductase: “Crystal structure of a short chain dehydrogenase homolog (target efi- 505321) from burkholderia multivorans…”. X-ray diffraction, 3 ligands (NAD, SO4, CL), 9 pockets (best druggability…
- PDB
- 4GLO
- Type
- protein
- Length
- 1,014 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier protein] reductase
- EC
- 1.1.1.100
- UniProt
- A9ANE0
- Ligands
- NAD, SO4, CL
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) | protein | 258 | 48% helix, 14% strand | A9ANE0 |
| C | 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) | protein | 248 | 46% helix, 14% strand | A9ANE0 |
| D | 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) | protein | 250 | 48% helix, 15% strand | A9ANE0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.87 | 0.92 | 49 | empty |
| 2 | 657 | 0.75 | 0.81 | 51 | NAD, SO4 |
| 3 | 681 | 0.74 | 0.80 | 51 | NAD, SO4 |
| 4 | 543 | 0.70 | 0.79 | 52 | NAD, SO4 |
| 5 | 535 | 0.69 | 0.79 | 52 | NAD, SO4 |
Interfaces
6 interfaces between chains.
- B–C · 1810 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1798 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1675 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1592 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 690 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4GLO · Crystal structure of a short chain dehydrogenase homolog (target EFI-505321) 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 A9ANE0
- Elsewhere: RCSB PDB 4GLO · PDBe 4GLO · UniProt A9ANE0
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