MolNFT v1 · #138994 · protein
VANILLATE/3-O-methylgallate O-demethylase, ligm, vanillate complex form
5X1J: “VANILLATE/3-O-methylgallate O-demethylase, ligm, vanillate complex form”. X-ray diffraction, 1 ligand (VNL), 12 pockets (best druggability 0.89). MolNFT v1 #138994 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X1J
- Type
- protein
- Length
- 1,361 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VANILLATE/3-O-methylgallate O-demethylase
- UniProt
- G2IQS7
- Ligands
- VNL
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | VANILLATE/3-O-methylgallate O-demethylase | protein | 455 | 27% helix, 28% strand | G2IQS7 |
| B | VANILLATE/3-O-methylgallate O-demethylase | protein | 451 | 27% helix, 28% strand | G2IQS7 |
Ligands and binding sites
- VNL · 4-hydroxy-3-methoxybenzoate · ligand · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.89 | 0.93 | 79 | empty |
| 2 | 895 | 0.82 | 0.84 | 79 | VNL |
| 3 | 393 | 0.73 | 0.83 | 49 | VNL |
| 4 | 369 | 0.72 | 0.83 | 47 | VNL |
| 5 | 295 | 0.56 | 0.76 | 47 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1911 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 358 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5X1J · Vanillate/3-O-methylgallate O-demethylase, LigM, vanillate complex form · the same entry in another collection · chain A against A, TM-score 1.00
- G2IQS7 · AlphaFold monomer V2.0 prediction for VANILLATE/3-O-methylgallate O-demethylase (G2IQS7) · a predicted model of the same protein · 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 G2IQS7
- Elsewhere: RCSB PDB 5X1J · PDBe 5X1J · UniProt G2IQS7
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