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Crystal structure of a T1-like thiolase (CoA-complex) from mycobacterium smegmatis

Analyse Crystal structure of a T1-like thiolase (CoA-complex) from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BZ4
Type: protein
Length: 4,778 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-ketothiolase
UniProt: A0QUH3
Ligands: COA
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 11 distinct chains · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-ketothiolase	protein	398	39% helix, 21% strand	A0QUH3
B	Beta-ketothiolase	protein	398	38% helix, 21% strand	A0QUH3
C	Beta-ketothiolase	protein	398	40% helix, 21% strand	A0QUH3
D	Beta-ketothiolase	protein	397	39% helix, 22% strand	A0QUH3
E	Beta-ketothiolase	protein	396	41% helix, 21% strand	A0QUH3
F	Beta-ketothiolase	protein	399	38% helix, 21% strand	A0QUH3
G	Beta-ketothiolase	protein	402	41% helix, 20% strand	A0QUH3
H, M	Beta-ketothiolase	protein	397	39% helix, 21% strand	A0QUH3
J	Beta-ketothiolase	protein	396	40% helix, 20% strand	A0QUH3
K	Beta-ketothiolase	protein	400	39% helix, 21% strand	A0QUH3
L	Beta-ketothiolase	protein	400	40% helix, 21% strand	A0QUH3

Ligands and binding sites

COA · Coenzyme A · ligand · 5 copies · chains B, A, D, F, G, E, H, K, L

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	107	0.79	0.98	32	empty
2	102	0.78	0.98	33	empty
3	105	0.78	0.98	30	empty
4	104	0.78	0.98	33	empty
5	109	0.78	0.97	32	empty

Interfaces

23 interfaces between chains.

E–F · 3056 Å² buried · 72 hydrogen bonds · protein-protein
L–M · 3043 Å² buried · 75 hydrogen bonds · protein-protein
A–B · 3043 Å² buried · 76 hydrogen bonds · protein-protein
J–K · 3020 Å² buried · 73 hydrogen bonds · protein-protein
G–H · 2973 Å² buried · 70 hydrogen bonds · protein-protein

Compared structures

5BZ4 · Crystal structure of a T1-like thiolase (CoA-complex) from Mycobacterium smegmatis · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0QUH3
Elsewhere: RCSB PDB 5BZ4 · PDBe 5BZ4 · UniProt A0QUH3

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