9UV6 | pdb_00009uv6

Encounter complex structure of E2N and Ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb9UV6/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-05-09 Released: 2025-07-23 
• Deposition Author(s): Gong, Z., Liu, M.L., Zhang, X., He, L.C., Zhao, Q., Zhang, L.H., Zhang, B.R.
• Funding Organization(s): Other government, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 240 
• Conformers Submitted: 3 
• Selection Criteria: structures with the lowest energy 

Literature

X-GAME: An Integrative Framework for Deciphering Protein-Protein Interactions in Living Cells

Gong, Z., Zhang, B.R., He, X.F., Zhong, B.W., Zhu, Y.L., Tan, K.N., Liu, Z., Chen, J., Liang, Z., Zhang, X., He, L.C., Zhang, Y.K., Zhang, L.H., Liu, M.L., Zhao, Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 25.99 kDa 
• Atom Count: 1,808 
• Modeled Residue Count: 224 
• Deposited Residue Count: 226 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 N	A	150	Homo sapiens	Mutation(s): 1  Gene Names: UBE2N, BLU EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens) Explore P61088  Go to UniProtKB:  P61088
PHAROS:  P61088 GTEx:  ENSG00000177889

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	76	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA80, UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EQF (Subject of Investigation/LOI)	C [auth A]	(5~{S},16~{S})-16-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylamino]-2,11,12,17-tetraoxa-5,8-diaza-1$l^{4}-manganatricyclo[6.3.3.3^{1,5}]heptadecane-3,10,13-trione C16 H22 Mn N4 O9 MONZMKOQRHPWJD-MERQFXBCSA-K

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 240 
• Conformers Submitted: 3 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Gong, Z., Liu, M.L., Zhang, X., He, L.C., Zhao, Q., Zhang, L.H., Zhang, B.R.

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Funding Organization	Location	Grant Number
Other government		XDB0540000
Other government		2021YFA1301501
Other government		2024YFC3405400
National Natural Science Foundation of China (NSFC)	China	22322411
National Natural Science Foundation of China (NSFC)	China	22374154
National Natural Science Foundation of China (NSFC)	China	22393931
National Natural Science Foundation of China (NSFC)	China	32088101

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release