9F7Z | pdb_00009f7z

Crystal structure of human 4-1BB/TNFRSF9 in complex with the anti-4-1BB DARPin protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 
    0.291 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

HUMAN TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 9 IN COMPLEX WITH LIGAND DARPIN HB01

Saltarella, I., Link, A., Lamanuzzi, A., Reichen, C., Robinson, J., Altamura, C., Solimando, A.G., Ria, R., Vacca, A., Frassanito, M.A., Desaphy, J.F.

To be published.

Macromolecule Content 

  • Total Structure Weight: 229.14 kDa 
  • Atom Count: 15,717 
  • Modeled Residue Count: 2,079 
  • Deposited Residue Count: 2,112 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-4-1BB DARPin
A, C, E, G, I
A, C, E, G, I, K, M, O
126synthetic constructMutation(s): 0 
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 9
B, D, F, H, J
B, D, F, H, J, L, N, P
138Homo 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

Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
Q
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G95595RA
GlyCosmos: G95595RA
GlyGen: G95595RA
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
R, S, T, U, W
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G44123WW
GlyCosmos: G44123WW
GlyGen: G44123WW
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
V
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G61843VN
GlyCosmos: G61843VN
GlyGen: G61843VN

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG


Download:Ideal Coordinates CCD File
X [auth N]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.291 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.33α = 90
b = 102.469β = 91.54
c = 167.366γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata 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
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release