MolNFT v1 · #47915 · protein
Crystal structure of the helicobacter pylori enoyl-acyl carrier protein reductase in complex with hydroxydiphenyl ether compounds, triclosan and diclosan
2PD4 · Enoyl-[acyl-carrier-protein] reductase [NADH]: “Crystal structure of the helicobacter pylori enoyl-acyl carrier protein reductase in complex with…”. X-ray diffraction, 2 ligands (NAD, DCN), 8 pockets (best druggability 0.84). MolNFT…
- PDB
- 2PD4
- Type
- protein
- Length
- 1,096 residues
- Chains
- 4
- 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
- O24990
- Ligands
- NAD, DCN
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 274 | 46% helix, 16% strand | O24990 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- DCN · Diclosan · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.84 | 0.85 | 62 | empty |
| 2 | 556 | 0.81 | 0.87 | 50 | NAD, DCN |
| 3 | 544 | 0.80 | 0.86 | 48 | NAD, DCN |
| 4 | 554 | 0.80 | 0.86 | 50 | NAD, DCN |
| 5 | 548 | 0.80 | 0.86 | 50 | NAD, DCN |
Interfaces
6 interfaces between chains.
- A–B · 1725 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1718 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1653 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1651 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1312 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2PD4 · Crystal Structure of the Helicobacter pylori Enoyl-Acyl Carrier Protein Reductase in… · the same entry in another collection · chain D against D, TM-score 1.00
- O24990 · AlphaFold monomer V2.0 prediction for enoyl-[acyl-carrier-protein] reductase [NADH] fabi… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O24990
- Elsewhere: RCSB PDB 2PD4 · PDBe 2PD4 · UniProt O24990
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