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Model of human anaphase-promoting COMPLEX/CYCLOSOME (APC15 deletion mutant), in complex with the mitotic checkpoint complex (APC/C-CDC20- mcc) based on cryo EM data at 4.8 ångström resolution

Analyse Model of human anaphase-promoting COMPLEX/CYCLOSOME (APC15 deletion mutant), in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5KHU
Type
protein
Length
8,453 residues
Chains
23
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Anaphase-promoting complex subunit 1; Anaphase-promoting complex subunit 11; Cell…
EC
2.7.11.1
UniProt
Q9H1A4, Q9NYG5, Q9UJX2, Q96DE5, P30260, Q8NHZ8, Q9UJX5, Q13042, Q9UM13, Q9BS18, Q9UJX6, Q9UJX4, O60566, Q12834, Q13257, Q9UJX3
Pockets
9 · best druggability 0.46

Structure

electron microscopy · 22 distinct chains · 0% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AAnaphase-promoting complex subunit 1protein13740% helix, 0% strandQ9H1A4
BAnaphase-promoting complex subunit 11protein160% helix, 0% strandQ9NYG5
CCell division cycle protein 23 homologprotein4630% helix, 0% strandQ9UJX2
EAnaphase-promoting complex subunit 16protein560% helix, 0% strandQ96DE5
FCell division cycle protein 27 homologprotein4730% helix, 0% strandP30260
G, WAnaphase-promoting complex subunit CDC26protein250% helix, 0% strandQ8NHZ8
HCell division cycle protein 27 homologprotein4790% helix, 0% strandP30260
IAnaphase-promoting complex subunit 4protein7060% helix, 0% strandQ9UJX5
JCell division cycle protein 16 homologprotein5040% helix, 0% strandQ13042
KCell division cycle protein 16 homologprotein4930% helix, 0% strandQ13042
LAnaphase-promoting complex subunit 10protein1690% helix, 0% strandQ9UM13
MAnaphase-promoting complex subunit 13protein430% helix, 0% strandQ9BS18
NAnaphase-promoting complex subunit 2protein6270% helix, 0% strandQ9UJX6
OAnaphase-promoting complex subunit 5protein6080% helix, 0% strandQ9UJX4
PCell division cycle protein 23 homologprotein4420% helix, 0% strandQ9UJX2
QMitotic checkpoint SERINE/THREONINE-protein kinase BUB1 beta (EC 2.7.11.1)protein2190% helix, 0% strandO60566
RCell division cycle protein 20 homologprotein3780% helix, 0% strandQ12834
SCell division cycle protein 20 homologprotein3330% helix, 0% strandQ12834
TMitotic spindle assembly checkpoint protein MAD2Aprotein1830% helix, 0% strandQ13257
UUnknownprotein90% helix, 0% strand—
XAnaphase-promoting complex subunit 7protein3960% helix, 0% strandQ9UJX3
YAnaphase-promoting complex subunit 7protein4320% helix, 0% strandQ9UJX3

Pockets

9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11710.460.7336empty
21300.400.7338empty
31120.400.7334empty
41070.390.7429empty
51050.380.7323empty

Interfaces

28 interfaces between chains.

  • B–N · 412 Ų buried · 0 hydrogen bonds · protein-protein
  • S–T · 241 Ų buried · 0 hydrogen bonds · protein-protein
  • A–O · 229 Ų buried · 0 hydrogen bonds · protein-protein
  • Q–R · 207 Ų buried · 0 hydrogen bonds · protein-protein
  • I–O · 167 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

  • 5KHU · Model of human Anaphase-promoting complex/Cyclosome (APC15 deletion mutant), in complex… · the same entry in another collection · chain L against L, TM-score 1.00

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