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MolNFT v1 · #124525 · protein

Model of human anaphase-promoting COMPLEX/CYCLOSOME complex (APC15 deletion mutant) in complex with the E2 UBE2C/UBCH10 poised for ubiquitin ligation to substrate (APC/C-CDC20-substrate-UBE2C)

5KHR · Anaphase-promoting complex subunit 1: “Model of human anaphase-promoting COMPLEX/CYCLOSOME complex (APC15 deletion mutant) in complex with the E2…”. Electron microscopy, 7 pockets (best druggability 0.41). MolNFT v1 #124525 on…

PDB
5KHR
Type
protein
Length
7,932 residues
Chains
21
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Anaphase-promoting complex subunit 1; Anaphase-promoting complex subunit 11; Cell…
EC
2.3.2.23, 2.3.2.24
UniProt
Q9H1A4, Q9NYG5, Q9UJX2, Q96DE5, P30260, Q8NHZ8, Q9UJX5, Q13042, Q9UM13, Q9BS18, Q9UJX6, Q9UJX4, O00762, Q12834, Q9UJX3
Pockets
7 · best druggability 0.41

Structure

electron microscopy · 20 distinct chains · 0% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AAnaphase-promoting complex subunit 1protein13910% helix, 0% strandQ9H1A4
BAnaphase-promoting complex subunit 11protein690% helix, 0% strandQ9NYG5
CCell division cycle protein 23 homologprotein4680% helix, 0% strandQ9UJX2
EAnaphase-promoting complex subunit 16protein560% helix, 0% strandQ96DE5
FCell division cycle protein 27 homologprotein4810% helix, 0% strandP30260
G, WAnaphase-promoting complex subunit CDC26protein250% helix, 0% strandQ8NHZ8
HCell division cycle protein 27 homologprotein4830% helix, 0% strandP30260
IAnaphase-promoting complex subunit 4protein6930% 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 10protein1740% helix, 0% strandQ9UM13
MAnaphase-promoting complex subunit 13protein470% helix, 0% strandQ9BS18
NAnaphase-promoting complex subunit 2protein6450% helix, 0% strandQ9UJX6
OAnaphase-promoting complex subunit 5protein6030% helix, 0% strandQ9UJX4
PCell division cycle protein 23 homologprotein4410% helix, 0% strandQ9UJX2
QUbiquitin-conjugating enzyme E2 C (EC 2.3.2.23, 2.3.2.24)protein1450% helix, 0% strandO00762
RCell division cycle protein 20 homologprotein3680% helix, 0% strandQ12834
SHSL1 peptideprotein100% helix, 0% strand—
XAnaphase-promoting complex subunit 7protein3960% helix, 0% strandQ9UJX3
YAnaphase-promoting complex subunit 7protein4150% helix, 0% strandQ9UJX3

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11220.410.7331empty
21100.390.7331empty
3710.320.7319empty
4680.310.7215empty
5600.300.7320empty

Interfaces

34 interfaces between chains.

  • A–O · 440 Ų buried · 0 hydrogen bonds · protein-protein
  • B–N · 350 Ų buried · 0 hydrogen bonds · protein-protein
  • X–Y · 224 Ų buried · 0 hydrogen bonds · protein-protein
  • I–O · 206 Ų buried · 0 hydrogen bonds · protein-protein
  • C–P · 165 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

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

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