Research workbench

S. cerevisiae apo phosphorylated APC/C

Analyse S. cerevisiae apo phosphorylated APC/C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8A61
Type: protein
Length: 7,203 residues
Chains: 17
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anaphase-promoting complex subunit CDC27; Anaphase-promoting complex subunit CDC16…
EC: 6.3.2.-
UniProt: P38042, P09798, P14724, Q12107, Q12440, Q12157, P53886, Q08683, P16522, Q12379, P40577, Q04601, P53068
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 17 distinct chains · 59% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F	Anaphase-promoting complex subunit CDC27	protein	502	77% helix, 0% strand	P38042
J	Anaphase-promoting complex subunit CDC16	protein	509	73% helix, 0% strand	P09798
K	Anaphase-promoting complex subunit CDC16	protein	505	74% helix, 0% strand	P09798
G	Anaphase-promoting complex subunit CDC26	protein	34	59% helix, 0% strand	P14724
W	Anaphase-promoting complex subunit CDC26	protein	30	57% helix, 0% strand	P14724
H	Anaphase-promoting complex subunit CDC27	protein	505	75% helix, 0% strand	P38042
E	Anaphase-promoting complex subunit 9	protein	130	56% helix, 2% strand	Q12107
T	Anaphase-promoting complex subunit 2	protein	650	65% helix, 6% strand	Q12440
U	Anaphase-promoting complex subunit 11 (EC 6.3.2.-)	protein	114	25% helix, 24% strand	Q12157
C	Anaphase-promoting complex subunit 1	protein	1406	45% helix, 13% strand	P53886
O	Anaphase-promoting complex subunit 5	protein	658	67% helix, 2% strand	Q08683
D	Anaphase-promoting complex subunit CDC23	protein	560	70% helix, 0% strand	P16522
P	Anaphase-promoting complex subunit CDC23	protein	556	71% helix, 0% strand	P16522
I	Anaphase-promoting complex subunit SWM1	protein	107	38% helix, 8% strand	Q12379
N	Anaphase-promoting complex subunit MND2	protein	96	44% helix, 4% strand	P40577
Q	Anaphase-promoting complex subunit 4	protein	623	39% helix, 24% strand	Q04601
A	Anaphase-promoting complex subunit DOC1	protein	218	16% helix, 28% strand	P53068

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	899	0.86	0.88	96	empty
2	1084	0.85	0.86	115	empty
3	1135	0.84	0.85	89	empty
4	1014	0.84	0.85	97	empty
5	858	0.83	0.85	95	empty

Interfaces

37 interfaces between chains.

O–Q · 3283 Å² buried · 37 hydrogen bonds · protein-protein
J–K · 2999 Å² buried · 40 hydrogen bonds · protein-protein
F–E · 2692 Å² buried · 28 hydrogen bonds · protein-protein
C–A · 2619 Å² buried · 24 hydrogen bonds · protein-protein
C–O · 2612 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

8A61 · S. cerevisiae apo phosphorylated APC/C · the same entry in another collection · chain O against O, 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 P38042
Every structure of UniProt P09798
Every structure of UniProt P14724
Every structure of UniProt Q12107
Every structure of UniProt Q12440
Every structure of UniProt Q12157
Every structure of UniProt P53886
Every structure of UniProt Q08683
Every structure of UniProt P16522
Every structure of UniProt Q12379
Every structure of UniProt P40577
Every structure of UniProt Q04601
Every structure of UniProt P53068
Elsewhere: RCSB PDB 8A61 · PDBe 8A61 · UniProt P38042 · UniProt P09798 · UniProt P14724 · UniProt Q12107 · UniProt Q12440 · UniProt Q12157 · UniProt P53886 · UniProt Q08683 · UniProt P16522 · UniProt Q12379 · UniProt P40577 · UniProt Q04601 · UniProt P53068

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