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Benzoylsuccinyl-CoA thiolase

Analyse Benzoylsuccinyl-CoA thiolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PXP
Type: protein
Length: 2,074 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2
Source: Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)
Molecule: Benzoylsuccinyl-CoA thiolase subunit
UniProt: Q39VG2, Q39VG1
Ligands: ZN
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · resolution 2 · 7 distinct chains · 29% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Benzoylsuccinyl-CoA thiolase subunit	protein	132	0% helix, 47% strand	Q39VG2
B, F	Benzoylsuccinyl-CoA thiolase subunit	protein	131	0% helix, 47% strand	Q39VG2
C	Benzoylsuccinyl-CoA thiolase subunit	protein	384	37% helix, 18% strand	Q39VG1
D	Benzoylsuccinyl-CoA thiolase subunit	protein	385	37% helix, 18% strand	Q39VG1
E	Benzoylsuccinyl-CoA thiolase subunit	protein	133	0% helix, 47% strand	Q39VG2
G	Benzoylsuccinyl-CoA thiolase subunit	protein	391	37% helix, 18% strand	Q39VG1
H	Benzoylsuccinyl-CoA thiolase subunit	protein	387	37% helix, 19% strand	Q39VG1

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, E, F

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	656	0.84	0.88	82	empty
2	515	0.82	0.88	73	empty
3	1014	0.80	0.82	92	empty
4	1050	0.79	0.81	82	empty
5	921	0.71	0.76	94	empty

Interfaces

12 interfaces between chains.

C–D · 1937 Å² buried · 39 hydrogen bonds · protein-protein
G–H · 1889 Å² buried · 39 hydrogen bonds · protein-protein
B–D · 1566 Å² buried · 28 hydrogen bonds · protein-protein
F–G · 1564 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 1527 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

7PXP · Benzoylsuccinyl-CoA thiolase · 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 Q39VG2
Every structure of UniProt Q39VG1
Elsewhere: RCSB PDB 7PXP · PDBe 7PXP · UniProt Q39VG2 · UniProt Q39VG1

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