8FT9 | pdb_00008ft9

Crystal structure of a new antigen receptor variable domain from nurse sharks

PDB DOI: https://doi.org/10.2210/pdb8FT9/pdb

Classification: ANTITOXIN
Organism(s): Ginglymostoma cirratum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-01-11 Released: 2025-04-02
Deposition Author(s): Yerabham, A.S.K., Hsieh, C.M., Fu, Y., Bou-Nader, C., Cachau, R., Zhang, J., Ho, M.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free:
0.278 (Depositor), 0.277 (DCC)
R-Value Work:
0.240 (Depositor), 0.240 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a new antigen receptor variable domain from nurse sharks

Yerabham, A.S.K., Fu, Y., Hsieh, C.M., Bou-Nader, C., Cachau, R., Zhang, J., Ho, M.

To be published.

Macromolecule Content

Total Structure Weight: 87.29 kDa
Atom Count: 5,203
Modeled Residue Count: 650
Deposited Residue Count: 768
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VNAR B6	A, B, C, D, E A, B, C, D, E, F	128	Ginglymostoma cirratum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth B] G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth D], O [auth D], P [auth E], R [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Q [auth F] MOL2 format, chain Q [auth F] mmCIF format, chain Q [auth F]	Q [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Q [auth F] Interactions & Density Focus chain Q [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.278 (Depositor), 0.277 (DCC)
R-Value Work: 0.240 (Depositor), 0.240 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.824	α = 90
b = 89.891	β = 90
c = 186.849	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	Z01 BC010891
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	ZIA BC010891
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	ZIC BC 011891
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	ZIADK075136