MolNFT v1 · #115605 · protein
The effect of valine to alanine mutation on inha enzyme crystallization pattern and substrate binding loop conformation and flexibility
5COQ · Enoyl-[acyl-carrier-protein] reductase [NADH]: “The effect of valine to alanine mutation on inha enzyme crystallization pattern and substrate binding loop…”. X-ray diffraction, 3 ligands (NAD, TCU, NA), 10 pockets (best druggability…
- PDB
- 5COQ
- Type
- protein
- Length
- 1,052 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
- M9TGV3
- Ligands
- NAD, TCU, NA
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 264 | 47% helix, 17% strand | M9TGV3 |
| B | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 268 | 47% helix, 17% strand | M9TGV3 |
| C | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 258 | 45% helix, 17% strand | M9TGV3 |
| D | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 262 | 47% helix, 18% strand | M9TGV3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- TCU · 5-hexyl-2-(2-methylphenoxy)phenol · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1155 | 0.83 | 0.84 | 56 | empty |
| 2 | 548 | 0.82 | 0.88 | 50 | NAD, TCU |
| 3 | 616 | 0.82 | 0.86 | 48 | NAD, TCU |
| 4 | 567 | 0.81 | 0.86 | 51 | NAD, TCU |
| 5 | 803 | 0.81 | 0.84 | 66 | NAD, TCU |
Interfaces
6 interfaces between chains.
- A–B · 1573 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1571 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1505 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1503 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 657 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5COQ · The effect of valine to alanine mutation on InhA enzyme crystallization pattern and… · 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 M9TGV3
- Elsewhere: RCSB PDB 5COQ · PDBe 5COQ · UniProt M9TGV3
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