Research workbench

SUCCINATE:COENZYME-a transferase (pig heart)

Analyse SUCCINATE:COENZYME-a transferase (pig heart) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1O9L
Type: protein
Length: 1,782 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Succinyl-COA\:3-ketoacid-coenzyme a transferase
EC: 2.8.3.5
UniProt: Q29551
Ligands: EMC, EMT
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Succinyl-COA\:3-ketoacid-coenzyme a transferase (EC 2.8.3.5)	protein	468	20% helix, 31% strand	Q29551
B	Succinyl-COA\:3-ketoacid-coenzyme a transferase (EC 2.8.3.5)	protein	425	23% helix, 32% strand	Q29551
C	Succinyl-COA\:3-ketoacid-coenzyme a transferase (EC 2.8.3.5)	protein	425	22% helix, 33% strand	Q29551
D	Succinyl-COA\:3-ketoacid-coenzyme a transferase (EC 2.8.3.5)	protein	464	21% helix, 32% strand	Q29551

Ligands and binding sites

EMC · Ethyl mercury ion · ligand · 7 copies · chains A, B, C, D
EMT · 2-(ethylmercuri-thio)-benzoic acid · ligand · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	256	0.84	0.96	37	empty
2	247	0.84	0.96	38	empty
3	528	0.73	0.81	67	empty
4	371	0.69	0.82	46	empty
5	271	0.67	0.83	42	EMT

Interfaces

4 interfaces between chains.

A–B · 2458 Å² buried · 46 hydrogen bonds · protein-protein
C–D · 2450 Å² buried · 42 hydrogen bonds · protein-protein
A–C · 462 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 96 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1O9L · Succinate:Coenzyme-A Transferase (pig heart) · the same entry in another collection · chain D against D, TM-score 1.00
Q29551 · AlphaFold monomer V2.0 prediction for succinyl-COA:3-ketoacid coenzyme a transferase 1… · a predicted model of the same protein · chain B 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 Q29551
Elsewhere: RCSB PDB 1O9L · PDBe 1O9L · UniProt Q29551

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