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Model of human anaphase-promoting COMPLEX/CYCLOSOME (APC/C-CDH1) with a cross linked ubiquitin variant-substrate-UBE2C (UBCH10) complex representing key features of multiubiquitination

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

PDB
5L9U
Type
protein
Length
8,055 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, 2.3.2.24
UniProt
Q9H1A4, Q9NYG5, Q9UJX2, P60006, Q96DE5, P30260, Q8NHZ8, Q9UJX5, Q13042, Q9UM13, Q9BS18, Q9UJX6, Q9UJX4, Q9UM11, P34244, Q63429, O00762, Q9UJX3
Pockets
4 · best druggability 0.39

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
AAnaphase-promoting complex subunit 1protein13420% helix, 0% strandQ9H1A4
BAnaphase-promoting complex subunit 11protein710% helix, 0% strandQ9NYG5
CCell division cycle protein 23 homologprotein4740% 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 4protein7190% helix, 0% strandQ9UJX5
JCell division cycle protein 16 homologprotein4990% helix, 0% strandQ13042
KCell division cycle protein 16 homologprotein4930% helix, 0% strandQ13042
LAnaphase-promoting complex subunit 10protein1760% helix, 0% strandQ9UM13
MAnaphase-promoting complex subunit 13protein490% helix, 0% strandQ9BS18
NAnaphase-promoting complex subunit 2protein6100% helix, 0% strandQ9UJX6
OAnaphase-promoting complex subunit 5protein6760% helix, 0% strandQ9UJX4
PCell division cycle protein 23 homologprotein4250% helix, 0% strandQ9UJX2
RFizzy-related protein homologprotein3850% helix, 0% strandQ9UM11
SHSL1(SUBSTRATE)_PEPTIDE-UBIQUITIN_VARIANT fusion (EC 2.7.11.1)protein860% helix, 0% strandP34244, Q63429
UUbiquitin-conjugating enzyme E2 C (EC 2.3.2.23, 2.3.2.24)protein1450% helix, 0% strandO00762
XAnaphase-promoting complex subunit 7protein3800% helix, 0% strandQ9UJX3
YAnaphase-promoting complex subunit 7protein3990% helix, 0% strandQ9UJX3

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11250.390.7230empty
21120.380.7328empty
3720.330.7325empty
4640.300.7323empty

Interfaces

38 interfaces between chains.

  • B–N · 409 Ų buried · 0 hydrogen bonds · protein-protein
  • A–O · 358 Ų buried · 0 hydrogen bonds · protein-protein
  • I–O · 213 Ų buried · 0 hydrogen bonds · protein-protein
  • X–Y · 167 Ų buried · 0 hydrogen bonds · protein-protein
  • A–L · 164 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

  • 5L9U · Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with a cross linked… · the same entry in another collection · chain K against K, TM-score 1.00

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