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Crystal structure of malonate decarboxylase from bordatella bronchiseptica

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

PDB: 3DG9
Type: protein
Length: 232 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arylmalonate decarboxylase
EC: 4.1.1.76
UniProt: Q05115
Ligands: PO4
Pockets: 1 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Arylmalonate decarboxylase (EC 4.1.1.76)	protein	232	48% helix, 16% strand	Q05115

Ligands and binding sites

PO4 · Phosphate ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	181	0.64	0.84	30	PO4

Compared structures

3DG9 · Crystal Structure of Malonate Decarboxylase from Bordatella bronchiseptica · the same entry in another collection · chain A against A, TM-score 1.00
Q05115 · AlphaFold monomer V2.0 prediction for arylmalonate decarboxylase (Q05115) · 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 Q05115
Elsewhere: RCSB PDB 3DG9 · PDBe 3DG9 · UniProt Q05115

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