Research workbench

Cryo-EM structure of combined apo phosphorylated apc

Analyse Cryo-EM structure of combined apo phosphorylated apc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5G05
Type: protein
Length: 8,027 residues
Chains: 20
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anaphase-promoting complex subunit 1; Anaphase-promoting complex subunit 11; Cell…
UniProt: Q9H1A4, Q9NYG5, Q9UJX2, P60006, Q96DE5, P30260, Q8NHZ8, Q9UJX5, Q13042, Q9UM13, Q2NKV2, Q9UJX6, Q9UJX4, Q9UJX3
Ligands: ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 20 distinct chains · 62% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Anaphase-promoting complex subunit 1	protein	1569	40% helix, 13% strand	Q9H1A4
B	Anaphase-promoting complex subunit 11	protein	84	13% helix, 24% strand	Q9NYG5
C	Cell division cycle protein 23 homolog	protein	524	76% helix, 0% strand	Q9UJX2
D	Anaphase-promoting complex subunit 15	protein	55	35% helix, 0% strand	P60006
E	Anaphase-promoting complex subunit 16	protein	56	84% helix, 0% strand	Q96DE5
F	Cell division cycle protein 27 homolog	protein	460	76% helix, 0% strand	P30260
G	Anaphase-promoting complex subunit CDC26	protein	25	40% helix, 0% strand	Q8NHZ8
H	Cell division cycle protein 27 homolog	protein	488	80% helix, 0% strand	P30260
I	Anaphase-promoting complex subunit 4	protein	723	35% helix, 25% strand	Q9UJX5
J	Cell division cycle protein 16 homolog	protein	504	76% helix, 0% strand	Q13042
K	Cell division cycle protein 16 homolog	protein	493	79% helix, 0% strand	Q13042
L	Anaphase-promoting complex subunit 10	protein	182	10% helix, 32% strand	Q9UM13
M	Anaphase-promoting complex subunit 13	protein	59	29% helix, 0% strand	Q2NKV2
N	Anaphase-promoting complex subunit 2	protein	604	67% helix, 2% strand	Q9UJX6
O	Anaphase-promoting complex subunit 5	protein	688	75% helix, 0% strand	Q9UJX4
P	Cell division cycle protein 23 homolog	protein	492	77% helix, 0% strand	Q9UJX2
T	Unidentified peptide	protein	15	0% helix, 0% strand	—
W	Anaphase-promoting complex subunit CDC26	protein	26	38% helix, 0% strand	Q8NHZ8
X	Anaphase-promoting complex subunit 7	protein	484	80% helix, 0% strand	Q9UJX3
Y	Anaphase-promoting complex subunit 7	protein	496	80% helix, 0% strand	Q9UJX3

Ligands and binding sites

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

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	980	0.88	0.89	94	empty
2	1114	0.87	0.88	115	empty
3	870	0.87	0.89	94	empty
4	976	0.84	0.86	87	empty
5	900	0.84	0.86	102	empty

Interfaces

47 interfaces between chains.

A–O · 5251 Å² buried · 44 hydrogen bonds · protein-protein
I–O · 3283 Å² buried · 26 hydrogen bonds · protein-protein
F–H · 2957 Å² buried · 16 hydrogen bonds · protein-protein
J–K · 2880 Å² buried · 40 hydrogen bonds · protein-protein
X–Y · 2838 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 isopeptide, 1 disulfide (isopeptide, disulfide).

Compared structures

5G05 · Cryo-EM structure of combined apo phosphorylated APC · the same entry in another collection · chain J against J, 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 Q9H1A4
Every structure of UniProt Q9NYG5
Every structure of UniProt Q9UJX2
Every structure of UniProt P60006
Every structure of UniProt Q96DE5
Every structure of UniProt P30260
Every structure of UniProt Q8NHZ8
Every structure of UniProt Q9UJX5
Every structure of UniProt Q13042
Every structure of UniProt Q9UM13
Every structure of UniProt Q2NKV2
Every structure of UniProt Q9UJX6
Every structure of UniProt Q9UJX4
Every structure of UniProt Q9UJX3
Elsewhere: RCSB PDB 5G05 · PDBe 5G05 · UniProt Q9H1A4 · UniProt Q9NYG5 · UniProt Q9UJX2 · UniProt P60006 · UniProt Q96DE5 · UniProt P30260 · UniProt Q8NHZ8 · UniProt Q9UJX5 · UniProt Q13042 · UniProt Q9UM13 · UniProt Q2NKV2 · UniProt Q9UJX6 · UniProt Q9UJX4 · UniProt Q9UJX3

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