MolNFT v1 · #93218 · protein
Crystal structure of a short chain dehydrogenase homolog (target efi- 505321) from burkholderia multivorans, with bound NADP and L-fucose
4GVX · 3-oxoacyl-[acyl-carrier protein] reductase: “Crystal structure of a short chain dehydrogenase homolog (target efi- 505321) from burkholderia multivorans…”. X-ray diffraction, 4 ligands (NAP, FUL, MG), 13 pockets (best druggability…
- PDB
- 4GVX
- Type
- protein
- Length
- 1,032 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
- NAP, FUL, MG, CL
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) | protein | 258 | 48% helix, 14% strand | A9ANE0 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- FUL · beta-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.77 | 0.87 | 43 | NAP, FUL |
| 2 | 385 | 0.77 | 0.86 | 46 | NAP, FUL |
| 3 | 376 | 0.76 | 0.86 | 42 | NAP, FUL |
| 4 | 391 | 0.76 | 0.86 | 45 | NAP, FUL |
| 5 | 266 | 0.50 | 0.74 | 28 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1799 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1580 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 540 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4GVX · 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 4GVX · PDBe 4GVX · UniProt A9ANE0
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