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MolNFT v1 · #124528 · protein

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

5KHU · Anaphase-promoting complex subunit 1: “Model of human anaphase-promoting COMPLEX/CYCLOSOME (APC15 deletion mutant), in complex with the mitotic…”. Electron microscopy, 9 pockets (best druggability 0.46). MolNFT v1 #124528 on…

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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