9RV5 | pdb_00009rv5

Crystal structure of SPSB2 SPRY domain in complex with linear TAT peptide

• PDB DOI: https://doi.org/10.2210/pdb9RV5/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-07-07 Released: 2025-08-06 
• Deposition Author(s): Lenz, C., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.199 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Crystal structure of SPSB2 SPRY domain in complex with linear TAT peptide

Lenz, C., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 52.82 kDa 
• Atom Count: 3,405 
• Modeled Residue Count: 403 
• Deposited Residue Count: 474 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPRY domain-containing SOCS box protein 2	A, C	217	Homo sapiens	Mutation(s): 0  Gene Names: SPSB2, GRCC9, SSB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99619 (Homo sapiens) Explore Q99619  Go to UniProtKB:  Q99619
PHAROS:  Q99619 GTEx:  ENSG00000111671

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tat Peptide	B, D	20	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	H [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	E [auth A], F [auth A], G [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.199 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.47	α = 90
b = 90.106	β = 97.47
c = 57.817	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Lenz, C., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	875510

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release