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Structure of CSY4 Apo-form

Analyse Structure of CSY4 Apo-form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6K5V
Type: protein
Length: 2,588 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.69
Source: Arabidopsis thaliana
Molecule: Citrate synthase 4, mitochondrial
EC: 2.3.3.16
UniProt: P20115
Ligands: CL
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · resolution 2.69 · 3 distinct chains · 62% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Citrate synthase 4, mitochondrial (EC 2.3.3.16)	protein	433	62% helix, 6% strand	P20115
B, D, E	Citrate synthase 4, mitochondrial (EC 2.3.3.16)	protein	430	62% helix, 6% strand	P20115
F	Citrate synthase 4, mitochondrial (EC 2.3.3.16)	protein	432	63% helix, 6% strand	P20115

Ligands and binding sites

CL · Chloride ion · ion · 6 copies · chains A, B, C, D, 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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	572	0.71	0.79	59	CL
2	551	0.69	0.79	55	CL
3	582	0.69	0.78	48	CL
4	547	0.69	0.79	45	CL
5	537	0.68	0.78	47	CL

Interfaces

8 interfaces between chains.

A–B · 4617 Å² buried · 61 hydrogen bonds · protein-protein
E–F · 4583 Å² buried · 60 hydrogen bonds · protein-protein
C–D · 4520 Å² buried · 52 hydrogen bonds · protein-protein
C–F · 334 Å² buried · 3 hydrogen bonds · protein-protein
A–F · 195 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6K5V · Structure of CSY4 apo-form · the same entry in another collection · chain F against F, TM-score 1.00
P20115 · AlphaFold monomer V2.0 prediction for citrate synthase 4, mitochondrial (P20115) · a predicted model of the same protein · chain D 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 P20115
Elsewhere: RCSB PDB 6K5V · PDBe 6K5V · UniProt P20115

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