Research workbench

CYTC3 with FE(II) and alpha-ketoglutarate

Analyse CYTC3 with FE(II) and alpha-ketoglutarate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GJB
Type: protein
Length: 531 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CYTC3
Ligands: AKG, FE2, SO4
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CYTC3	protein	260	21% helix, 31% strand	—
B	CYTC3	protein	271	20% helix, 29% strand	—

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · 3 copies · chains A, B
FE2 · Fe (II) ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B
ACT · Acetate ion · additive · 8 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1061	0.80	0.82	90	FE2, AKG, ACT, SO4
2	221	0.54	0.78	38	empty

Interfaces

1 interface between chains.

A–B · 1492 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

3GJB · CytC3 with Fe(II) and alpha-ketoglutarate · 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
Elsewhere: RCSB PDB 3GJB · PDBe 3GJB

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