8YAT | pdb_00008yat

SOD1, Nanobody1, Nanobody2 and Nanobody3 complex

• PDB DOI: https://doi.org/10.2210/pdb8YAT/pdb

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


• Deposited: 2024-02-10 Released: 2025-02-12 
• Deposition Author(s): Cheng, S.
• 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: 3.94 Å
• R-Value Free: 
  0.368 (Depositor), 0.365 (DCC) 
• R-Value Work: 
  0.303 (Depositor), 0.303 (DCC) 
• R-Value Observed: 
  0.308 (Depositor) 

Literature

SOD1,Nanobody1 and Nanobody2 complex

Cheng, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 225.22 kDa 
• Atom Count: 15,601 
• Modelled Residue Count: 2,084 
• Deposited Residue Count: 2,108 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, E, I, M	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
NB1	B, F, J, N	117	Vicugna pacos	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NB2	C, G, K, O	130	Camelus dromedarius	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NB3	D, H, L, P	127	Camelus dromedarius	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	Q [auth A], R [auth E], S [auth I], T [auth M]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.94 Å
• R-Value Free:  0.368 (Depositor), 0.365 (DCC) 
• R-Value Work:  0.303 (Depositor), 0.303 (DCC) 
• R-Value Observed: 0.308 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 377.129	α = 90
b = 46.672	β = 90
c = 156.949	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Cheng, S.

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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: 2025-02-12
  Type: Initial release