GL1X · GenesisL1 explorer

Research workbench

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)

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

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

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.