Research workbench
Crystal structure of B. pseudomallei fabi in complex with NAD and PT408
Analyse Crystal structure of B. pseudomallei fabi in complex with NAD and PT408 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I9M
- Type
- protein
- Length
- 771 residues
- Chains
- 3
- 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
- A0A069B9A4
- Ligands
- NAD, 69K
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 257 | 50% helix, 16% strand | A0A069B9A4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
- 69K · 5-ethyl-4-fluoro-2-[(2-methylpyridin-3-yl)oxy]phenol · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.81 | 0.87 | 50 | NAD, 69K |
| 2 | 526 | 0.80 | 0.86 | 46 | NAD, 69K |
| 3 | 542 | 0.79 | 0.85 | 48 | NAD, 69K |
| 4 | 513 | 0.63 | 0.76 | 45 | empty |
| 5 | 179 | 0.45 | 0.75 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1381 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 168 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5I9M · Crystal structure of B. pseudomallei FabI in complex with NAD and PT408 · 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 A0A069B9A4
- Elsewhere: RCSB PDB 5I9M · PDBe 5I9M · UniProt A0A069B9A4
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