9LNZ | pdb_00009lnz

Crystal Structure of Intracellular B30.2 Domain of VpBTN3 in Complex with HMBPP-08

PDB DOI: https://doi.org/10.2210/pdb9LNZ/pdb

Classification: SIGNALING PROTEIN
Organism(s): Vicugna pacos
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-22 Released: 2025-05-21
Deposition Author(s): Yang, Y.Y., Yi, S.M., Zhang, M.T., Chen, C.-C., Guo, R.-T.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.200 (Depositor), 0.209 (DCC)
R-Value Work:
0.155 (Depositor), 0.167 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Intracellular B30.2 Domain of VpBTN3 in Complex with HMBPP-08

Yang, Y.Y., Yi, S.M., Zhang, M.T., Chen, C.-C., Guo, R.-T.

To be published.

Macromolecule Content

Total Structure Weight: 54.69 kDa
Atom Count: 3,532
Modeled Residue Count: 382
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Butyrophylin 3	A, B	242	Vicugna pacos	Mutation(s): 0 Gene Names: Btn3
UniProt
Find proteins for A0A345DF50 (Vicugna pacos) Explore A0A345DF50 Go to UniProtKB: A0A345DF50
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A345DF50
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
99C (Subject of Investigation/LOI) Query on 99C Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	(2E)-3-(hydroxymethyl)-4-(4-methylphenyl)but-2-en-1-yl trihydrogen diphosphate C₁₂ H₁₈ O₈ P₂ UZMNPEQMXYMHTH-WUXMJOGZSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A], D [auth A], E [auth A], H [auth B], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]