8K33

SOD1 and Nanobody1 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

SOD1 and Nanobody1 complex

Cheng, S.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]
A,
C,
E,
G,
I,
K,
L,
N,
P,
S [auth Y],
U,
W
153Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00441
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NB1
B, D, F, H, J
B, D, F, H, J, M, O, Q, R, T, V, X
117Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth G]
CA [auth I]
DA [auth K]
EA [auth L]
AA [auth E],
BA [auth G],
CA [auth I],
DA [auth K],
EA [auth L],
FA [auth N],
GA [auth P],
HA [auth Y],
IA [auth U],
JA [auth W],
Y [auth A],
Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.208α = 90
b = 119.67β = 91.64
c = 130.707γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2024-07-17 
    • Deposition Author(s): Cheng, S.
Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2021YFA0805200
National Science Foundation (NSF, China)China32070939
National Science Foundation (NSF, China)China82030106

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary