GL1X · GenesisL1 explorer

Research workbench

Model of human anaphase-promoting COMPLEX/CYCLOSOME (APC/C-CDH1) with E2 UBE2S poised for polyubiquitination where UBE2S, APC2, and APC11 are modeled into low resolution density

Analyse Model of human anaphase-promoting COMPLEX/CYCLOSOME (APC/C-CDH1) with E2 UBE2S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5L9T
Type
protein
Length
8,038 residues
Chains
22
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, 2.3.2.23
UniProt
Q9H1A4, Q9NYG5, Q9UJX2, P60006, Q96DE5, P30260, Q8NHZ8, Q9UJX5, Q13042, Q9UM13, Q9BS18, Q9UJX6, Q9UJX4, Q9UM11, P0CG47, P34244, Q16763, Q9UJX3
Pockets
7 · best druggability 0.43

Structure

electron microscopy · 21 distinct chains · 0% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AAnaphase-promoting complex subunit 1protein13800% helix, 0% strandQ9H1A4
BAnaphase-promoting complex subunit 11protein680% helix, 0% strandQ9NYG5
CCell division cycle protein 23 homologprotein4750% helix, 0% strandQ9UJX2
DAnaphase-promoting complex subunit 15protein550% helix, 0% strandP60006
EAnaphase-promoting complex subunit 16protein560% helix, 0% strandQ96DE5
FCell division cycle protein 27 homologprotein4820% 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 4protein7270% 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 10protein1700% helix, 0% strandQ9UM13
MAnaphase-promoting complex subunit 13protein420% helix, 0% strandQ9BS18
NAnaphase-promoting complex subunit 2protein5460% helix, 0% strandQ9UJX6
OAnaphase-promoting complex subunit 5protein6850% helix, 0% strandQ9UJX4
PCell division cycle protein 23 homologprotein4430% helix, 0% strandQ9UJX2
RFizzy-related protein homologprotein3850% helix, 0% strandQ9UM11
SUBIQUITIN_VARIANT-HSL1(SUBSTRATE) fusion (EC 2.7.11.1)protein840% helix, 0% strandP0CG47, P34244
TUbiquitin-conjugating enzyme E2 S (EC 2.3.2.23)protein970% helix, 0% strandQ16763
XAnaphase-promoting complex subunit 7protein3970% helix, 0% strandQ9UJX3
YAnaphase-promoting complex subunit 7protein4160% 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
11490.430.7336empty
21060.380.7330empty
3760.330.7322empty
4700.320.7324empty
5600.290.7219empty

Interfaces

37 interfaces between chains.

  • A–O · 410 Ų buried · 0 hydrogen bonds · protein-protein
  • B–N · 332 Ų buried · 0 hydrogen bonds · protein-protein
  • I–O · 215 Ų buried · 0 hydrogen bonds · protein-protein
  • X–Y · 176 Ų buried · 0 hydrogen bonds · protein-protein
  • A–L · 164 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

  • 5L9T · Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with E2 UBE2S poised for… · the same entry in another collection · chain K against K, TM-score 1.00

Analyse

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