MolNFT v1 · #134976 · protein
Crystal structure of sphingomonas paucimobilis aryl O-demethylase ligm
5TL4 · VANILLATE/3-O-methylgallate O-demethylase: “Crystal structure of sphingomonas paucimobilis aryl O-demethylase ligm”. X-ray diffraction, 3 ligands (NA, CL, NH4), 17 pockets (best druggability 0.88). MolNFT v1 #134976 on GenesisL1: 3D…
- PDB
- 5TL4
- Type
- protein
- Length
- 1,817 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VANILLATE/3-O-methylgallate O-demethylase
- UniProt
- Q60FX1
- Ligands
- NA, CL, NH4
- Pockets
- 17 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | VANILLATE/3-O-methylgallate O-demethylase | protein | 461 | 27% helix, 26% strand | Q60FX1 |
| B | VANILLATE/3-O-methylgallate O-demethylase | protein | 447 | 28% helix, 27% strand | Q60FX1 |
| D | VANILLATE/3-O-methylgallate O-demethylase | protein | 448 | 27% helix, 27% strand | Q60FX1 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- NH4 · Ammonium ion · ion
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.88 | 0.91 | 79 | empty |
| 2 | 727 | 0.88 | 0.92 | 78 | empty |
| 3 | 558 | 0.73 | 0.81 | 52 | CL, NA |
| 4 | 531 | 0.73 | 0.81 | 56 | CL, NA |
| 5 | 522 | 0.72 | 0.81 | 59 | CL, NA |
Interfaces
3 interfaces between chains.
- A–B · 1894 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1892 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 133 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5TL4 · Crystal structure of Sphingomonas paucimobilis aryl O-demethylase LigM · the same entry in another collection · chain C against C, 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 Q60FX1
- Elsewhere: RCSB PDB 5TL4 · PDBe 5TL4 · UniProt Q60FX1
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