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Crystal structure of putataive short-chain DEHYDROGENASE/REDUCTASE (fabg) from klebsiella pneumoniae subsp. pneumoniae ntuh-K2044 in complex with NADH
Analyse Crystal structure of putataive short-chain DEHYDROGENASE/REDUCTASE (fabg) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TZP
- Type
- protein
- Length
- 1,962 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-acp reductase
- EC
- 1.1.1.100
- UniProt
- A0A332H2K8
- Ligands
- NAI, K, CL
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | 3-oxoacyl-acp reductase (EC 1.1.1.100) | protein | 245 | 49% helix, 18% strand | A0A332H2K8 |
| E | 3-oxoacyl-acp reductase (EC 1.1.1.100) | protein | 244 | 49% helix, 18% strand | A0A332H2K8 |
| G | 3-oxoacyl-acp reductase (EC 1.1.1.100) | protein | 247 | 49% helix, 18% strand | A0A332H2K8 |
| H | 3-oxoacyl-acp reductase (EC 1.1.1.100) | protein | 246 | 47% helix, 17% strand | A0A332H2K8 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, C, E, G
- K · Potassium ion · metal · 4 copies · chains A, D, B, C, E, G
- CL · Chloride ion · ion · 14 copies · chains A, B, D, C, E, F, G, H
- GOL · Glycerol · additive · 15 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, D, B, C, H, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.85 | 0.86 | 84 | K, GOL, EDO |
| 2 | 686 | 0.77 | 0.82 | 87 | EDO |
| 3 | 584 | 0.76 | 0.83 | 55 | empty |
| 4 | 476 | 0.75 | 0.83 | 45 | NAI |
| 5 | 444 | 0.74 | 0.84 | 46 | NAI |
Interfaces
11 interfaces between chains.
- A–B · 1872 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1862 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 1846 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1838 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1418 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 modified (engineered).
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 A0A332H2K8
- Elsewhere: RCSB PDB 7TZP · PDBe 7TZP · UniProt A0A332H2K8
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