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Structural studies of acetoacetate decarboxylase

Analyse Structural studies of acetoacetate decarboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BGT
Type: protein
Length: 977 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable acetoacetate decarboxylase
EC: 4.1.1.4
UniProt: Q7NSA6
Pockets: 10 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Probable acetoacetate decarboxylase (EC 4.1.1.4)	protein	244	14% helix, 55% strand	Q7NSA6
D	Probable acetoacetate decarboxylase (EC 4.1.1.4)	protein	245	15% helix, 55% strand	Q7NSA6

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	111	0.78	0.97	30	empty
2	192	0.73	0.89	37	empty
3	243	0.72	0.87	36	empty
4	203	0.72	0.88	43	empty
5	719	0.66	0.75	87	empty

Interfaces

5 interfaces between chains.

A–B · 2632 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 441 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 434 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 423 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 376 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 modified (engineered).

Compared structures

3BGT · Structural Studies of Acetoacetate Decarboxylase · the same entry in another collection · chain D against D, TM-score 1.00
Q7NSA6 · AlphaFold monomer V2.0 prediction for probable acetoacetate decarboxylase (Q7NSA6) · a predicted model of the same protein · chain B 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 Q7NSA6
Elsewhere: RCSB PDB 3BGT · PDBe 3BGT · UniProt Q7NSA6

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