Research workbench
Crystal structure of vanillin bound to co-LSD4 from sphingobium sp. strain syk-6
Analyse Crystal structure of vanillin bound to co-LSD4 from sphingobium sp. strain syk-6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XM9
- Type
- protein
- Length
- 479 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dioxygenase
- EC
- 1.13.11.-
- UniProt
- G2IQT9
- Ligands
- V55, CO, MG
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dioxygenase (EC 1.13.11.-) | protein | 479 | 9% helix, 40% strand | G2IQT9 |
Ligands and binding sites
- V55 · 4-hydroxy-3-methoxybenzaldehyde · ligand · chains A
- CO · Cobalt (II) ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 8 copies · chains A
- ACT · Acetate ion · additive · 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 | 470 | 0.75 | 0.83 | 43 | empty |
| 2 | 490 | 0.70 | 0.80 | 45 | V55 |
| 3 | 122 | 0.58 | 0.85 | 34 | DMS |
| 4 | 102 | 0.48 | 0.81 | 21 | DMS |
Compared structures
- 6XM9 · Crystal structure of vanillin bound to Co-LSD4 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 G2IQT9
- Elsewhere: RCSB PDB 6XM9 · PDBe 6XM9 · UniProt G2IQT9
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