Research workbench

Atomic structure of the apaf-1 apoptosome

Analyse Atomic structure of the apaf-1 apoptosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3JBT
Type: protein
Length: 8,736 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apoptotic protease-activating factor 1; Cytochrome C
UniProt: O14727, P00004
Ligands: DTP, HEM, MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 2 distinct chains · 26% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K, M	Apoptotic protease-activating factor 1	protein	1144	25% helix, 24% strand	O14727
B, D, F, H, J, L, N	Cytochrome C	protein	104	41% helix, 2% strand	P00004

Ligands and binding sites

DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 7 copies · chains A, C, E, G, I, K, M
HEM · Protoporphyrin IX containing Fe · ligand · 7 copies · chains B, D, F, H, J, L, N
MG · Magnesium ion · metal · 7 copies · chains A, C, E, G, I, K, M

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	919	0.86	0.88	130	empty
2	1057	0.85	0.86	97	HEM
3	1138	0.85	0.86	133	empty
4	1163	0.85	0.86	142	empty
5	1052	0.85	0.86	98	HEM

Interfaces

14 interfaces between chains.

K–M · 1536 Å² buried · 27 hydrogen bonds · protein-protein
C–E · 1535 Å² buried · 27 hydrogen bonds · protein-protein
I–K · 1532 Å² buried · 27 hydrogen bonds · protein-protein
E–G · 1532 Å² buried · 27 hydrogen bonds · protein-protein
G–I · 1531 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 35 disulfide, 14 cofactor (disulfide, heme attachment).

Compared structures

3JBT · Atomic structure of the Apaf-1 apoptosome · the same entry in another collection · chain K against K, 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 O14727
Every structure of UniProt P00004
Elsewhere: RCSB PDB 3JBT · PDBe 3JBT · UniProt O14727 · UniProt P00004

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.