MolNFT v1 · #191162 · protein

S. cerevisiae APC/C-CDH1 complex

8A3T · Anaphase-promoting complex subunit CDC27: “S. cerevisiae APC/C-CDH1 complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.87). MolNFT v1 #191162 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8A3T
Type: protein
Length: 7,661 residues
Chains: 19
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, P53068, A0A6A5PYD7, A0A8H4BYV4, P53886, Q08683, P16522, Q12379, P40577, Q04601, Q12440, Q12157
Ligands: ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 19 distinct chains · 57% helix, 9% 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	72% helix, 0% strand	P09798
K	Anaphase-promoting complex subunit CDC16	protein	505	74% helix, 0% strand	P09798
G	Anaphase-promoting complex subunit CDC26	protein	35	63% helix, 0% strand	P14724
W	Anaphase-promoting complex subunit CDC26	protein	37	65% helix, 0% strand	P14724
H	Anaphase-promoting complex subunit CDC27	protein	505	76% helix, 0% strand	P38042
E	Anaphase-promoting complex subunit 9	protein	130	59% helix, 2% strand	Q12107
A	Anaphase-promoting complex subunit DOC1	protein	219	15% helix, 31% strand	P53068
B	CDH1 isoform 1	protein	440	15% helix, 34% strand	A0A6A5PYD7
S	HSL1 isoform 1	protein	6	0% helix, 0% strand	A0A8H4BYV4
C	Anaphase-promoting complex subunit 1	protein	1410	44% 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	70% helix, 0% strand	P16522
I	Anaphase-promoting complex subunit SWM1	protein	111	41% helix, 8% strand	Q12379
N	Anaphase-promoting complex subunit MND2	protein	96	47% helix, 4% strand	P40577
Q	Anaphase-promoting complex subunit 4	protein	623	39% helix, 24% strand	Q04601
T	Anaphase-promoting complex subunit 2	protein	645	66% helix, 6% strand	Q12440
U	Anaphase-promoting complex subunit 11 (EC 6.3.2.-)	protein	114	25% helix, 24% strand	Q12157

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains U

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	1163	0.87	0.88	134	empty
2	903	0.86	0.88	86	empty
3	988	0.85	0.86	104	empty
4	1072	0.83	0.84	118	empty
5	953	0.83	0.84	83	empty

Interfaces

48 interfaces between chains.

O–Q · 3388 Å² buried · 36 hydrogen bonds · protein-protein
C–O · 3168 Å² buried · 21 hydrogen bonds · protein-protein
J–K · 3047 Å² buried · 45 hydrogen bonds · protein-protein
F–H · 2658 Å² buried · 21 hydrogen bonds · protein-protein
F–E · 2628 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

8A3T · S. cerevisiae APC/C-Cdh1 complex · the same entry in another collection · chain C against C, 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 P53068
Every structure of UniProt A0A6A5PYD7
Every structure of UniProt A0A8H4BYV4
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 Q12440
Every structure of UniProt Q12157
Elsewhere: RCSB PDB 8A3T · PDBe 8A3T · UniProt P38042 · UniProt P09798 · UniProt P14724 · UniProt Q12107 · UniProt P53068 · UniProt A0A6A5PYD7 · UniProt A0A8H4BYV4 · UniProt P53886 · UniProt Q08683 · UniProt P16522 · UniProt Q12379 · UniProt P40577 · UniProt Q04601 · UniProt Q12440 · UniProt Q12157

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