Research workbench
VANILLATE/3-O-methylgallate O-demethylase, ligm, protocatechuate- tetrahydrofolate complex form
Analyse VANILLATE/3-O-methylgallate O-demethylase, ligm, protocatechuate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X1M
- Type
- protein
- Length
- 1,358 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
- DHB, THG
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VANILLATE/3-O-methylgallate O-demethylase | protein | 456 | 27% helix, 27% strand | G2IQS7 |
| B | VANILLATE/3-O-methylgallate O-demethylase | protein | 447 | 28% helix, 27% strand | G2IQS7 |
| C | VANILLATE/3-O-methylgallate O-demethylase | protein | 455 | 26% helix, 27% strand | G2IQS7 |
Ligands and binding sites
- DHB · 3,4-dihydroxybenzoic acid · ligand · 4 copies · chains A, B, C
- THG · (6S)-5,6,7,8-tetrahydrofolate · ligand · 2 copies · chains B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · chains B
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 | 770 | 0.89 | 0.93 | 81 | empty |
| 2 | 837 | 0.81 | 0.83 | 81 | DHB, TRS |
| 3 | 388 | 0.73 | 0.84 | 45 | THG, DHB |
| 4 | 539 | 0.72 | 0.80 | 51 | THG, DHB |
| 5 | 196 | 0.51 | 0.77 | 27 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1867 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 326 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5X1M · Vanillate/3-O-methylgallate O-demethylase, LigM, protocatechuate-tetrahydrofolate complex… · 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 B 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 5X1M · PDBe 5X1M · UniProt G2IQS7
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