MolNFT v1 · #124661 · protein
Crystal structure of thioacyl intermediate in 2-aminomuconate 6- semialdehyde dehydrogenase N169A
5KLO · 2-aminomuconate 6-semialdehyde dehydrogenase: “Crystal structure of thioacyl intermediate in 2-aminomuconate 6- semialdehyde dehydrogenase N169A”. X-ray diffraction, 3 ligands (2VS, NAD, NA), 12 pockets (best druggability 0.86).…
- PDB
- 5KLO
- Type
- protein
- Length
- 1,933 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-aminomuconate 6-semialdehyde dehydrogenase
- UniProt
- Q83V33
- Ligands
- 2VS, NAD, NA
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-aminomuconate 6-semialdehyde dehydrogenase | protein | 484 | 42% helix, 23% strand | Q83V33 |
| B, C, D | 2-aminomuconate 6-semialdehyde dehydrogenase | protein | 483 | 42% helix, 23% strand | Q83V33 |
Ligands and binding sites
- 2VS · (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoic acid · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.86 | 0.89 | 108 | empty |
| 2 | 844 | 0.85 | 0.88 | 66 | empty |
| 3 | 1197 | 0.84 | 0.85 | 110 | empty |
| 4 | 792 | 0.79 | 0.83 | 97 | empty |
| 5 | 417 | 0.76 | 0.85 | 57 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2708 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 2704 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 806 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 806 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 804 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5KLO · Crystal structure of thioacyl intermediate in 2-aminomuconate 6-semialdehyde… · 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 Q83V33
- Elsewhere: RCSB PDB 5KLO · PDBe 5KLO · UniProt Q83V33
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