MolNFT v2 · #214173 · protein
Crystal structure of 3-oxoacyl-ACP reductase FabG in complex with NADP+ and 3-keto-octanoyl-ACP from Helicobacter pylori in an inactive form that priors the acyl substrate delivery
8JFH · 3-oxoacyl-[acyl-carrier-protein] reductase: “Crystal structure of 3-oxoacyl-ACP reductase FabG in complex with NADP+ and 3-keto-octanoyl-ACP from…”. X-ray diffraction at 1.8, 3 ligands (NAP, UHC, PN7), 8 pockets (best druggability…
- PDB
- 8JFH
- Type
- protein
- Length
- 1,107 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Helicobacter pylori
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] reductase; Acyl carrier protein
- EC
- 1.1.1.100
- UniProt
- G2M827, Q5EDC8
- Ligands
- NAP, UHC, PN7
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.8 · 5 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) | protein | 237 | 49% helix, 16% strand | G2M827 |
| B | 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) | protein | 234 | 47% helix, 17% strand | G2M827 |
| C, D | 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) | protein | 238 | 47% helix, 17% strand | G2M827 |
| E | Acyl carrier protein | protein | 79 | 61% helix, 3% strand | Q5EDC8 |
| F | Acyl carrier protein | protein | 81 | 62% helix, 2% strand | Q5EDC8 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, D
- UHC · ~{S}-[2-[3-[[(2~{S})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] 3-oxidanylideneoctanethioate · ligand · chains E
- PN7 · N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide · ligand · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.84 | 0.86 | 70 | empty |
| 2 | 1174 | 0.73 | 0.77 | 113 | NAP |
| 3 | 50 | 0.66 | 0.96 | 24 | empty |
| 4 | 505 | 0.62 | 0.75 | 53 | empty |
| 5 | 103 | 0.61 | 0.87 | 21 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1737 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1676 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1525 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1519 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 361 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 G2M827
- Every structure of UniProt Q5EDC8
- Elsewhere: RCSB PDB 8JFH · PDBe 8JFH · UniProt G2M827 · UniProt Q5EDC8
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