Research workbench
Crystal structure of lige in complex with glutathione (gsh) from sphingobium sp. strain syk-6
Analyse Crystal structure of lige in complex with glutathione (gsh) from sphingobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YAN
- Type
- protein
- Length
- 1,005 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-etherase
- UniProt
- G2IN93
- Ligands
- GSH
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-etherase | protein | 252 | 50% helix, 10% strand | G2IN93 |
| B | Beta-etherase | protein | 250 | 49% helix, 10% strand | G2IN93 |
| D | Beta-etherase | protein | 251 | 50% helix, 10% strand | G2IN93 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.72 | 0.80 | 74 | empty |
| 2 | 329 | 0.59 | 0.77 | 39 | GSH |
| 3 | 243 | 0.58 | 0.78 | 33 | GSH |
| 4 | 248 | 0.57 | 0.78 | 30 | GSH |
| 5 | 258 | 0.56 | 0.77 | 30 | GSH |
Interfaces
4 interfaces between chains.
- C–D · 1099 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1097 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 737 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YAN · Crystal structure of LigE in complex with glutathione (GSH) from Sphingobium sp. strain… · 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 G2IN93
- Elsewhere: RCSB PDB 4YAN · PDBe 4YAN · UniProt G2IN93
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