8K3L

SOD1 and Nanobody3 complex

• PDB DOI: https://doi.org/10.2210/pdb8K3L/pdb

• Classification: OXIDOREDUCTASE/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Camelus dromedarius
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-16 Released: 2024-07-17 
• Deposition Author(s): Cheng, S., Liu, R., Ding, Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.235 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

SOD1 and Nanobody1 complex

Shihao, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 119.24 kDa 
• Atom Count: 8,526 
• Modelled Residue Count: 1,097 
• Deposited Residue Count: 1,120 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, C, E, G	153	Homo sapiens	Mutation(s): 0  Gene Names: SOD1 EC: 1.15.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens) Explore P00441  Go to UniProtKB:  P00441
PHAROS:  P00441 GTEx:  ENSG00000142168

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NB3	B, D, F, H	127	Camelus dromedarius	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	J [auth A], L [auth C], N [auth E], P [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	I [auth A], K [auth C], M [auth E], O [auth G]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.235 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.214	α = 90
b = 62.442	β = 90
c = 314.928	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Cheng, S., Liu, R., Ding, Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFA0805200
National Science Foundation (NSF, China)	China	32070939
National Science Foundation (NSF, China)	China	82030106

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release