MolNFT v1 · #121921 · protein
Crystal structure of B. pseudomallei fabi in complex with NAD and PT408
5I9M · Enoyl-[acyl-carrier-protein] reductase [NADH]: “Crystal structure of B. pseudomallei fabi in complex with NAD and PT408”. X-ray diffraction, 2 ligands (NAD, 69K), 8 pockets (best druggability 0.81). MolNFT v1 #121921 on GenesisL1…
- 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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