9HQ5 | pdb_00009hq5

Crystal structure of Tetraspanin CD63mutant Large Extracellular Loop (LEL) in complex with sybody SB3

PDB DOI: https://doi.org/10.2210/pdb9HQ5/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens, synthetic construct
Expression System: Drosophila melanogaster, Bacteria
Mutation(s): Yes

Deposited: 2024-12-16 Released: 2025-11-19
Deposition Author(s): Nagarathinam, K., Krey, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.292 (Depositor), 0.290 (DCC)
R-Value Work:
0.245 (Depositor), 0.243 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Models: in silico, experimental
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This is version 1.0 of the entry. See complete history.

Literature

Evolutionary relationship of Tetraspanins

Nagarathinam, K., Karakulova, D., Thiyagaraj, D., Krey, T.

To be published.

Macromolecule Content

Total Structure Weight: 28.42 kDa
Atom Count: 1,606
Modeled Residue Count: 214
Deposited Residue Count: 252
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD63 antigen	A	108	Homo sapiens	Mutation(s): 3 Gene Names: CD63, MLA1, TSPAN30
UniProt & NIH Common Fund Data Resources
Find proteins for P08962 (Homo sapiens) Explore P08962 Go to UniProtKB: P08962
PHAROS: P08962 GTEx: ENSG00000135404
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08962
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sybody SB3	B	144	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.292 (Depositor), 0.290 (DCC)
R-Value Work: 0.245 (Depositor), 0.243 (DCC)
R-Value Observed: 0.247 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.23	α = 90
b = 65.23	β = 90
c = 138.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Nagarathinam, K.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-11-19
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.