MolNFT v1 · #105060 · protein
Crystal structure of 5-carboxyvanillate decarboxylase LIGW2 (target efi-505250) from novosphingobium aromaticivorans dsm 12444 complexed with manganese
4QTG: “Crystal structure of 5-carboxyvanillate decarboxylase LIGW2 (target efi-505250) from novosphingobium…”. X-ray diffraction, 1 ligand (MN), 5 pockets (best druggability 0.76). MolNFT v1 #105060 on GenesisL1: 3D structure, binding…
- PDB
- 4QTG
- Type
- protein
- Length
- 697 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-carboxyvanillate decarboxylase
- UniProt
- Q2GA79
- Ligands
- MN
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-carboxyvanillate decarboxylase | protein | 348 | 50% helix, 10% strand | Q2GA79 |
| B | 5-carboxyvanillate decarboxylase | protein | 349 | 51% helix, 10% strand | Q2GA79 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.76 | 0.97 | 30 | empty |
| 2 | 100 | 0.76 | 0.96 | 31 | empty |
| 3 | 51 | 0.47 | 0.85 | 23 | GOL |
| 4 | 58 | 0.31 | 0.76 | 13 | empty |
| 5 | 71 | 0.30 | 0.74 | 15 | GOL |
Interfaces
1 interface between chains.
- A–B · 3023 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4QTG · CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 (TARGET EFI-505250) FROM… · 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 Q2GA79
- Elsewhere: RCSB PDB 4QTG · PDBe 4QTG · UniProt Q2GA79
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