MolNFT v1 · #152912 · protein
The crystal structure of sulfoacetaldehyde reductase from klebsiella oxytoca
6IXJ: “The crystal structure of sulfoacetaldehyde reductase from klebsiella oxytoca”. X-ray diffraction, 2 ligands (NDP, 8X3), 14 pockets (best druggability 0.87). MolNFT v1 #152912 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6IXJ
- Type
- protein
- Length
- 3,011 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfoacetaldehyde reductase
- EC
- 1.1.1.313
- UniProt
- D3U1D9
- Ligands
- NDP, 8X3
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, H, I, J, K, L | Sulfoacetaldehyde reductase (EC 1.1.1.313) | protein | 251 | 43% helix, 20% strand | D3U1D9 |
| C | Sulfoacetaldehyde reductase (EC 1.1.1.313) | protein | 250 | 46% helix, 15% strand | D3U1D9 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- 8X3 · 2-hydroxyethylsulfonic acid · ligand · 12 copies · chains A, I, B, H, C, D, E, L, F, J, G, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.87 | 0.89 | 128 | NDP, 8X3 |
| 2 | 1156 | 0.87 | 0.88 | 133 | NDP, 8X3 |
| 3 | 143 | 0.80 | 0.97 | 36 | empty |
| 4 | 508 | 0.80 | 0.86 | 51 | NDP, 8X3 |
| 5 | 510 | 0.79 | 0.86 | 62 | NDP, 8X3 |
Interfaces
19 interfaces between chains.
- F–K · 1888 Ų buried · 23 hydrogen bonds · protein-protein
- B–I · 1860 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1859 Ų buried · 23 hydrogen bonds · protein-protein
- A–H · 1857 Ų buried · 24 hydrogen bonds · protein-protein
- H–I · 1493 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 6IXJ · The crystal structure of sulfoacetaldehyde reductase from Klebsiella oxytoca · the same entry in another collection · chain L against L, 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 D3U1D9
- Elsewhere: RCSB PDB 6IXJ · PDBe 6IXJ · UniProt D3U1D9
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