MolNFT v1 · #105002 · protein
High-resolution crystal structure of 5-carboxyvanillate decarboxylase (target efi-505250) from novosphingobium aromaticivorans dsm 12444 complexed with manganese and 4-hydroxy-3-methoxy-5-nitrobenzoic acid
4QRN: “High-resolution crystal structure of 5-carboxyvanillate decarboxylase (target efi-505250) from…”. X-ray diffraction, 3 ligands (1DF, MN, CL), 9 pockets (best druggability 0.77). MolNFT v1 #105002 on GenesisL1: 3D structure, binding…
- PDB
- 4QRN
- Type
- protein
- Length
- 1,398 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-carboxyvanillate decarboxylase
- UniProt
- Q2GA79
- Ligands
- 1DF, MN, CL
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-carboxyvanillate decarboxylase | protein | 352 | 52% helix, 10% strand | Q2GA79 |
| B, C | 5-carboxyvanillate decarboxylase | protein | 348 | 51% helix, 10% strand | Q2GA79 |
| D | 5-carboxyvanillate decarboxylase | protein | 350 | 52% helix, 10% strand | Q2GA79 |
Ligands and binding sites
- 1DF · 4-hydroxy-3-methoxy-5-nitrobenzoic acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.77 | 0.98 | 30 | 1DF |
| 2 | 99 | 0.76 | 0.97 | 30 | 1DF |
| 3 | 88 | 0.76 | 0.97 | 28 | 1DF |
| 4 | 50 | 0.66 | 0.96 | 18 | 1DF |
| 5 | 51 | 0.47 | 0.85 | 22 | GOL, CL |
Interfaces
2 interfaces between chains.
- C–D · 3023 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 3010 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4QRN · HIGH-RESOLUTION CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE (TARGET EFI-505250)… · 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 4QRN · PDBe 4QRN · UniProt Q2GA79
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