3IE4 | pdb_00003ie4

b-glucan binding domain of Drosophila GNBP3 defines a novel family of pattern recognition receptor

PDB DOI: https://doi.org/10.2210/pdb3IE4/pdb

Classification: IMMUNE SYSTEM
Organism(s): Drosophila melanogaster
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2009-07-22 Released: 2009-08-18
Deposition Author(s): Mishima, Y., Coste, F., Kellenberger, C., Roussel, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.198 (Depositor), 0.225 (DCC)
R-Value Work:
0.165 (Depositor), 0.202 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The N-terminal domain of drosophila gram-negative binding protein 3 (GNBP3) defines a novel family of fungal pattern recognition receptors

Mishima, Y., Quintin, J., Aimanianda, V., Kellenberger, C., Coste, F., Clavaud, C., Hetru, C., Hoffmann, J.A., Latge, J.P., Ferrandon, D., Roussel, A.

To be published.

Macromolecule Content

Total Structure Weight: 24.9 kDa
Atom Count: 1,818
Modeled Residue Count: 202
Deposited Residue Count: 214
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gram-Negative Binding Protein 3	A, B	107	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for Q9NHA8 (Drosophila melanogaster) Explore Q9NHA8 Go to UniProtKB: Q9NHA8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NHA8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN 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 F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth B] C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	I [auth B], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.198 (Depositor), 0.225 (DCC)
R-Value Work: 0.165 (Depositor), 0.202 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.53	α = 90
b = 30.68	β = 107.57
c = 51.65	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHENIX	model building
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-08-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-08-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations