Research workbench
Crystal structure of ligl in complex with NADH and gge from sphingobium sp. strain syk-6
Analyse Crystal structure of ligl in complex with NADH and gge from sphingobium sp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YAI
- Type
- protein
- Length
- 546 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C alpha-dehydrogenase
- UniProt
- C0SUJ9
- Ligands
- NAI, GGE, MG
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C alpha-dehydrogenase | protein | 273 | 54% helix, 14% strand | C0SUJ9 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- GGE · (1S,2R)-1-(4-hydroxy-3-methoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol · ligand · chains B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.78 | 0.86 | 55 | NAI |
| 2 | 429 | 0.78 | 0.86 | 46 | NAI, GGE |
| 3 | 238 | 0.56 | 0.78 | 23 | empty |
| 4 | 52 | 0.24 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2602 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4YAI · Crystal structure of LigL in complex with NADH and GGE from Sphingobium sp. strain SYK-6 · 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 C0SUJ9
- Elsewhere: RCSB PDB 4YAI · PDBe 4YAI · UniProt C0SUJ9
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