Research workbench

Cryo-EM structure of the APC/C-CDC20-CDK2-CYCLINA2-CKS2 complex, the D2 box class

Analyse Cryo-EM structure of the APC/C-CDC20-CDK2-CYCLINA2-CKS2 complex, the D2 box… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Q6H
Type: protein
Length: 8,550 residues
Chains: 21
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anaphase-promoting complex subunit 10; Anaphase-promoting complex subunit 15; APC1…
UniProt: Q9UM13, P60006, Q9UJX6, Q9UJX5, Q9UJX4, Q13042, Q9NYG5, Q8NHZ8, Q9BS18, Q96DE5, P30260, Q9UJX3, Q9UJX2, Q12834, P20248
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 21 distinct chains · 56% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Anaphase-promoting complex subunit 10	protein	179	12% helix, 44% strand	Q9UM13
D	Anaphase-promoting complex subunit 15	protein	56	36% helix, 0% strand	P60006
A	APC1	protein	1551	38% helix, 15% strand	—
N	Anaphase-promoting complex subunit 2	protein	653	59% helix, 2% strand	Q9UJX6
I	Anaphase-promoting complex subunit 4	protein	729	31% helix, 27% strand	Q9UJX5
O	Anaphase-promoting complex subunit 5	protein	703	73% helix, 0% strand	Q9UJX4
K	Cell division cycle protein 16 homolog	protein	518	70% helix, 0% strand	Q13042
C	Anaphase-promoting complex subunit 11	protein	84	13% helix, 11% strand	Q9NYG5
G	Anaphase-promoting complex subunit CDC26	protein	27	52% helix, 0% strand	Q8NHZ8
W	Anaphase-promoting complex subunit CDC26	protein	26	46% helix, 0% strand	Q8NHZ8
M	Anaphase-promoting complex subunit 13	protein	61	20% helix, 0% strand	Q9BS18
H	Anaphase-promoting complex subunit 16	protein	57	82% helix, 0% strand	Q96DE5
J	Cell division cycle protein 27 homolog	protein	496	76% helix, 0% strand	P30260
P	Cell division cycle protein 27 homolog	protein	484	75% helix, 0% strand	P30260
Q	Cell division cycle protein 16 homolog	protein	504	72% helix, 0% strand	Q13042
Y	Anaphase-promoting complex subunit 7	protein	499	76% helix, 0% strand	Q9UJX3
U	Cell division cycle protein 23 homolog	protein	515	71% helix, 0% strand	Q9UJX2
V	Cell division cycle protein 23 homolog	protein	530	69% helix, 0% strand	Q9UJX2
Z	Anaphase-promoting complex subunit 7	protein	486	72% helix, 0% strand	Q9UJX3
R	Cell division cycle protein 20 homolog	protein	375	8% helix, 38% strand	Q12834
S	Cyclin-A2	protein	17	0% helix, 0% strand	P20248

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	1075	0.88	0.89	111	empty
2	887	0.87	0.90	89	empty
3	904	0.83	0.85	92	empty
4	985	0.83	0.84	87	empty
5	1121	0.83	0.84	96	empty

Interfaces

56 interfaces between chains.

A–O · 5708 Å² buried · 49 hydrogen bonds · protein-protein
I–O · 3384 Å² buried · 25 hydrogen bonds · protein-protein
J–P · 2965 Å² buried · 23 hydrogen bonds · protein-protein
K–Q · 2828 Å² buried · 45 hydrogen bonds · protein-protein
Y–Z · 2668 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6Q6H · Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, the D2 box class · the same entry in another collection · chain M against M, 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 Q9UM13
Every structure of UniProt P60006
Every structure of UniProt Q9UJX6
Every structure of UniProt Q9UJX5
Every structure of UniProt Q9UJX4
Every structure of UniProt Q13042
Every structure of UniProt Q9NYG5
Every structure of UniProt Q8NHZ8
Every structure of UniProt Q9BS18
Every structure of UniProt Q96DE5
Every structure of UniProt P30260
Every structure of UniProt Q9UJX3
Every structure of UniProt Q9UJX2
Every structure of UniProt Q12834
Every structure of UniProt P20248
Elsewhere: RCSB PDB 6Q6H · PDBe 6Q6H · UniProt Q9UM13 · UniProt P60006 · UniProt Q9UJX6 · UniProt Q9UJX5 · UniProt Q9UJX4 · UniProt Q13042 · UniProt Q9NYG5 · UniProt Q8NHZ8 · UniProt Q9BS18 · UniProt Q96DE5 · UniProt P30260 · UniProt Q9UJX3 · UniProt Q9UJX2 · UniProt Q12834 · UniProt P20248

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