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

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)

wwPDB Validation 3D Report Full Report

Validation slider image for 9RV5

This is version 1.0 of the entry. See complete history.

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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99619
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth C]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-06

Deposition Author(s):

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	875510

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.