8GYE | pdb_00008gye

Crystal Structure of the 4-1BB in complex with ZG033 Fab

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2022-09-22 Released: 2023-09-27 
  • Deposition Author(s): Zhu, M., Cheng, L.S., Gao, Y.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.277 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Crystal Structure of the 4-1BB in complex with ZG033 Fab

Zhu, M., Cheng, L.S., Gao, Y.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 9A,
B [auth D]		174Homo sapiensMutation(s): 0 
Gene Names: TNFRSF9, CD137, ILA
UniProt & NIH Common Fund Data Resources
Find proteins for Q07011 (Homo sapiens)
Explore Q07011 
Go to UniProtKB:  Q07011
PHAROS:  Q07011
GTEx:  ENSG00000049249 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07011
Glycosylation
Glycosylation Sites: 1
Go to GlyGen: Q07011-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ZG033 Fab H chainC [auth B],
E		220Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ZG033 Fab L chainD [auth C],
F		214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.021α = 90
b = 65.913β = 82.495
c = 83.643γ = 74.822
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)ChinaU1632124
National Natural Science Foundation of China (NSFC)China31621002
National Natural Science Foundation of China (NSFC)China31270770
Ministry of Science and Technology (MoST, China)China2017YFA0503600
Ministry of Science and Technology (MoST, China)China2017YFA0504903

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Derived calculations
  • Version 1.2: 2024-11-20
    Changes: Structure summary