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Ferulic acid decarboxylase (FDC1)

Analyse Ferulic acid decarboxylase (FDC1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4S13
Type: protein
Length: 3,875 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferulic acid decarboxylase 1
EC: 4.1.1.-
UniProt: Q03034
Ligands: 4VP
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 7 distinct chains · 32% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ferulic acid decarboxylase 1 (EC 4.1.1.-)	protein	472	32% helix, 24% strand	Q03034
B	Ferulic acid decarboxylase 1 (EC 4.1.1.-)	protein	476	31% helix, 24% strand	Q03034
C, F	Ferulic acid decarboxylase 1 (EC 4.1.1.-)	protein	501	32% helix, 24% strand	Q03034
D	Ferulic acid decarboxylase 1 (EC 4.1.1.-)	protein	480	32% helix, 25% strand	Q03034
E	Ferulic acid decarboxylase 1 (EC 4.1.1.-)	protein	492	32% helix, 24% strand	Q03034
G	Ferulic acid decarboxylase 1 (EC 4.1.1.-)	protein	472	32% helix, 24% strand	Q03034
H	Ferulic acid decarboxylase 1 (EC 4.1.1.-)	protein	481	31% helix, 25% strand	Q03034

Ligands and binding sites

4VP · 4-ethenylphenol · ligand · 5 copies · chains A, C, E, F, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	601	0.84	0.89	81	4VP
2	1182	0.84	0.85	117	empty
3	694	0.83	0.86	64	4VP
4	776	0.79	0.83	57	4VP
5	941	0.79	0.81	77	empty

Interfaces

14 interfaces between chains.

G–H · 3610 Å² buried · 43 hydrogen bonds · protein-protein
B–E · 3537 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 3520 Å² buried · 38 hydrogen bonds · protein-protein
D–F · 3495 Å² buried · 38 hydrogen bonds · protein-protein
B–D · 413 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4S13 · Ferulic Acid Decarboxylase (FDC1) · the same entry in another collection · chain H against H, TM-score 1.00
Q03034 · AlphaFold monomer V2.0 prediction for ferulic acid decarboxylase 1 (Q03034) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q03034
Elsewhere: RCSB PDB 4S13 · PDBe 4S13 · UniProt Q03034

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