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Insights into anaphase promoting complex tpr subdomain assembly from a CDC26-APC6 structure

Analyse Insights into anaphase promoting complex tpr subdomain assembly from a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HYM
Type: protein
Length: 1,954 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anaphase-promoting complex subunit CDC26; Cell division cycle protein 16 homolog
UniProt: Q8NHZ8, Q13042
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 6 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I	Anaphase-promoting complex subunit CDC26	protein	26	46% helix, 0% strand	Q8NHZ8
B, D, F, J	Cell division cycle protein 16 homolog	protein	301	71% helix, 0% strand	Q13042
C, K	Anaphase-promoting complex subunit CDC26	protein	23	22% helix, 0% strand	Q8NHZ8
G	Anaphase-promoting complex subunit CDC26	protein	25	32% helix, 0% strand	Q8NHZ8
H	Cell division cycle protein 16 homolog	protein	302	71% helix, 0% strand	Q13042
L	Cell division cycle protein 16 homolog	protein	299	70% helix, 0% strand	Q13042

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	789	0.74	0.79	85	empty
2	750	0.73	0.79	79	empty
3	771	0.73	0.78	86	empty
4	821	0.72	0.77	88	empty
5	149	0.72	0.90	27	empty

Interfaces

12 interfaces between chains.

I–J · 1728 Å² buried · 21 hydrogen bonds · protein-protein
K–L · 1719 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1716 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1713 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 1705 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 66 modified (engineered).

Compared structures

3HYM · Insights into Anaphase Promoting Complex TPR subdomain assembly from a CDC26-APC6… · the same entry in another collection · chain L against L, 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 Q8NHZ8
Every structure of UniProt Q13042
Elsewhere: RCSB PDB 3HYM · PDBe 3HYM · UniProt Q8NHZ8 · UniProt Q13042

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