Research workbench
The effect of valine to alanine mutation on inha enzyme crystallization pattern and substrate binding loop conformation and flexibility
Analyse The effect of valine to alanine mutation on inha enzyme crystallization pattern… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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