Research workbench
Crystal structure of fabi-NAD complex from candidatus liberibacter asiaticus
Analyse Crystal structure of fabi-NAD complex from candidatus liberibacter asiaticus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NK5
- Type
- protein
- Length
- 1,548 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-[acyl-carrier-protein] reductase [NADH]
- EC
- 1.3.1.9
- UniProt
- M4Q2P0
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 258 | 47% helix, 14% strand | M4Q2P0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.86 | 0.88 | 86 | empty |
| 2 | 1130 | 0.82 | 0.83 | 97 | empty |
| 3 | 1186 | 0.82 | 0.83 | 113 | NAD |
| 4 | 543 | 0.81 | 0.87 | 50 | NAD |
| 5 | 577 | 0.80 | 0.85 | 51 | NAD |
Interfaces
10 interfaces between chains.
- E–F · 1648 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1628 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1619 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 1619 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 1614 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4NK5 · Crystal structure of FabI-NAD complex from Candidatus Liberibacter asiaticus · 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 M4Q2P0
- Elsewhere: RCSB PDB 4NK5 · PDBe 4NK5 · UniProt M4Q2P0
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