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Crystal structure of gallic acid decarboxylase from arxula adeninivorans

Analyse Crystal structure of gallic acid decarboxylase from arxula adeninivorans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KD9
Type: protein
Length: 2,027 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gallate decarboxylase
UniProt: A0A060TAG5
Ligands: K
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 7 distinct chains · 34% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gallate decarboxylase	protein	231	31% helix, 34% strand	A0A060TAG5
B, F	Gallate decarboxylase	protein	225	32% helix, 34% strand	A0A060TAG5
C	Gallate decarboxylase	protein	227	33% helix, 33% strand	A0A060TAG5
D, G	Gallate decarboxylase	protein	226	34% helix, 35% strand	A0A060TAG5
E	Gallate decarboxylase	protein	219	37% helix, 34% strand	A0A060TAG5
H	Gallate decarboxylase	protein	222	35% helix, 33% strand	A0A060TAG5
I	Gallate decarboxylase	protein	226	32% helix, 35% strand	A0A060TAG5

Ligands and binding sites

K · Potassium ion · metal · 3 copies · chains A, B, D, C, E, F, G, H, I

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	1099	0.83	0.84	118	empty
2	114	0.79	0.98	29	empty
3	112	0.78	0.98	27	empty
4	88	0.78	0.99	24	empty
5	99	0.77	0.97	29	empty

Interfaces

17 interfaces between chains.

H–I · 1872 Å² buried · 25 hydrogen bonds · protein-protein
C–F · 1849 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 1838 Å² buried · 31 hydrogen bonds · protein-protein
E–F · 1810 Å² buried · 29 hydrogen bonds · protein-protein
B–D · 1803 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

7KD9 · Crystal Structure of Gallic Acid Decarboxylase from Arxula adeninivorans · 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 A0A060TAG5
Elsewhere: RCSB PDB 7KD9 · PDBe 7KD9 · UniProt A0A060TAG5

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