Research workbench

Cryo-EM structure of the APC/C-CDC20-CDK2-CYCLINA2-CKS2 complex, the D1 box class

Analyse Cryo-EM structure of the APC/C-CDC20-CDK2-CYCLINA2-CKS2 complex, the D1 box… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Q6G
Type: protein
Length: 8,576 residues
Chains: 21
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell division cycle protein 20 homolog; Cyclin-A2; Anaphase-promoting complex subunit 10…
UniProt: Q12834, P20248, Q9UM13, P60006, Q9H1A4, Q9UJX6, Q9UJX5, Q9UJX4, Q13042, Q9NYG5, Q8NHZ8, Q9BS18, Q96DE5, P30260, Q9UJX3, Q9UJX2
Pockets: 20 · best druggability 0.89

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	Cell division cycle protein 20 homolog	protein	382	8% helix, 39% strand	Q12834
S	Cyclin-A2	protein	31	0% helix, 0% strand	P20248
L	Anaphase-promoting complex subunit 10	protein	179	11% helix, 42% strand	Q9UM13
D	Anaphase-promoting complex subunit 15	protein	56	36% helix, 0% strand	P60006
A	Anaphase-promoting complex subunit 1,ANAPHASE-promoting complex subunit 1	protein	1553	39% helix, 15% strand	Q9H1A4
N	Anaphase-promoting complex subunit 2	protein	656	59% helix, 1% strand	Q9UJX6
I	Anaphase-promoting complex subunit 4	protein	729	30% helix, 25% strand	Q9UJX5
O	Anaphase-promoting complex subunit 5	protein	703	73% helix, 0% strand	Q9UJX4
K	Cell division cycle protein 16 homolog	protein	518	71% helix, 0% strand	Q13042
C	Anaphase-promoting complex subunit 11	protein	84	10% helix, 7% 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	16% helix, 3% strand	Q9BS18
H	Anaphase-promoting complex subunit 16	protein	57	79% 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	74% helix, 0% strand	P30260
Q	Cell division cycle protein 16 homolog	protein	504	71% 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	70% helix, 0% strand	Q9UJX2
Z	Anaphase-promoting complex subunit 7	protein	486	73% helix, 0% strand	Q9UJX3

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	989	0.89	0.90	103	empty
2	1161	0.87	0.88	108	empty
3	704	0.83	0.87	88	empty
4	355	0.82	0.92	50	empty
5	925	0.82	0.84	84	empty

Interfaces

56 interfaces between chains.

A–O · 5649 Å² buried · 57 hydrogen bonds · protein-protein
I–O · 3390 Å² buried · 36 hydrogen bonds · protein-protein
J–P · 2955 Å² buried · 24 hydrogen bonds · protein-protein
K–Q · 2819 Å² buried · 41 hydrogen bonds · protein-protein
Y–Z · 2693 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6Q6G · Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, the D1 box class · 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 Q12834
Every structure of UniProt P20248
Every structure of UniProt Q9UM13
Every structure of UniProt P60006
Every structure of UniProt Q9H1A4
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
Elsewhere: RCSB PDB 6Q6G · PDBe 6Q6G · UniProt Q12834 · UniProt P20248 · UniProt Q9UM13 · UniProt P60006 · UniProt Q9H1A4 · UniProt Q9UJX6 · UniProt Q9UJX5 · UniProt Q9UJX4 · UniProt Q13042 · UniProt Q9NYG5 · UniProt Q8NHZ8 · UniProt Q9BS18 · UniProt Q96DE5 · UniProt P30260 · UniProt Q9UJX3 · UniProt Q9UJX2

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