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MolNFT v1 · #125469 · protein

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

5L9T · Anaphase-promoting complex subunit 1: “Model of human anaphase-promoting COMPLEX/CYCLOSOME (APC/C-CDH1) with E2 UBE2S poised for polyubiquitination…”. Electron microscopy, 7 pockets (best druggability 0.43). MolNFT v1 #125469 on…

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

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