PDB-9wnw: beta-lactoglobulin in complex with Perfluorodecanoic acid (PFDA)

ID or keywords:

Entry

Database: PDB / ID: 9wnw

Title

beta-lactoglobulin in complex with Perfluorodecanoic acid (PFDA)

Components

Beta-lactoglobulin

Keywords

LIPID BINDING PROTEIN / beta-lactoglobulin / Perfluorodecanoic acid (PFDA)

Function / homology

Function and homology information

retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function

Biological species

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Verma, S. / Kumar, P.

Funding support

India, 1items

Citation

Journal: Biochemistry / Year: 2026
Title: Structural Insights into PFAS-beta-Lactoglobulin-Binding Mechanism Mediating PFAS Toxicity.
Authors: Verma, S. / Singh, A. / Ramirez Orozco, R.S. / Vukovic, L. / Narayan, M. / Kumar, P.

History

Deposition	Sep 5, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 15, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9wnw.cif.gz	100.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9wnw.ent.gz		Display	PDB format
PDBx/mmJSON format	9wnw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wn/9wnw ftp://data.pdbj.org/pub/pdb/validation_reports/wn/9wnw	HTTPS FTP

-
Related structure data

Related structure data	9wnvC 9wnxC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (5) #13 - Jan 2001 Alcohol Dehydrogenase similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #78 - Jun 2006 Luciferase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Beta-lactoglobulin

hetero molecules

19.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	53.023, 53.023, 111.157
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Beta-lactoglobulin / Beta-LG Mass: 18329.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02754
#2: Chemical	ChemComp-EOH / ETHANOL Mass: 46.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O
#3: Chemical	ChemComp-A1BLY / nonadecafluorodecanoic acid Mass: 514.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀HF₁₉O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.46746182 Å³/Da / Density % sol: 50.1821747 % / Description: Cube shaped
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion Details: 1.8 M sodium phosphate monobasic monohydrate and potassium phosphate dibasic at pH 8.2

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
Detector	Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 13, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54184 Å / Relative weight: 1
Reflection	Resolution: 2→28.84 Å / Num. obs: 12824 / % possible obs: 100 % / Redundancy: 14.39 % / CC_1/2: 1 / Net I/σ(I): 23.9
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 10.95 % / Mean I/σ(I) obs: 4.1 / Num. unique obs: 943 / CC_1/2: 0.903 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
CrysalisPro		data reduction
CrysalisPro		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2→22.495 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.934 / SU B: 9.587 / SU ML: 0.124 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / ESU R Free: 0.165 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2384	638	4.992 %
R_work	0.1886	12143	-
all	0.191	-	-
obs	-	12781	99.844 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 38.765 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.024 Å²	0.012 Å²	0 Å²
2-	-	0.024 Å²	-0 Å²
3-	-	-	-0.077 Å²

Refinement step

Cycle: LAST / Resolution: 2→22.495 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1249	0	50	26	1325

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	1405
X-RAY DIFFRACTION	r_angle_refined_deg	1.974	1.845	1923
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.93	5	178
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.393	5	3
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.334	10	270
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.973	10	56
X-RAY DIFFRACTION	r_chiral_restr	0.134	0.2	229
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1012
X-RAY DIFFRACTION	r_nbd_refined	0.269	0.2	699
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	923
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.289	0.2	79
X-RAY DIFFRACTION	r_metal_ion_refined	0.024	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.289	0.2	87
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.198	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	2.613	2.446	678
X-RAY DIFFRACTION	r_mcangle_it	3.858	4.349	858
X-RAY DIFFRACTION	r_scbond_it	4.463	3.04	727
X-RAY DIFFRACTION	r_scangle_it	6.698	5.442	1061
X-RAY DIFFRACTION	r_lrange_it	9.835	29.775	2181

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.052	0.283	38	0.206	896	X-RAY DIFFRACTION	100
2.052-2.108	0.26	34	0.231	849	X-RAY DIFFRACTION	100
2.108-2.168	0.344	42	0.24	822	X-RAY DIFFRACTION	100
2.168-2.234	0.31	55	0.222	805	X-RAY DIFFRACTION	100
2.234-2.307	0.291	40	0.198	796	X-RAY DIFFRACTION	100
2.307-2.387	0.25	23	0.207	760	X-RAY DIFFRACTION	100
2.387-2.476	0.338	38	0.215	730	X-RAY DIFFRACTION	100
2.476-2.576	0.278	34	0.211	711	X-RAY DIFFRACTION	100
2.576-2.689	0.266	55	0.215	666	X-RAY DIFFRACTION	100
2.689-2.818	0.266	35	0.214	656	X-RAY DIFFRACTION	100
2.818-2.968	0.247	42	0.213	615	X-RAY DIFFRACTION	100
2.968-3.144	0.224	39	0.193	583	X-RAY DIFFRACTION	100
3.144-3.357	0.244	25	0.181	571	X-RAY DIFFRACTION	99.8325
3.357-3.619	0.207	26	0.187	522	X-RAY DIFFRACTION	100
3.619-3.954	0.229	12	0.164	493	X-RAY DIFFRACTION	100
3.954-4.404	0.198	34	0.146	449	X-RAY DIFFRACTION	100
4.404-5.053	0.193	25	0.139	387	X-RAY DIFFRACTION	99.5169
5.053-6.112	0.187	18	0.187	355	X-RAY DIFFRACTION	100
6.112-8.341	0.27	17	0.185	278	X-RAY DIFFRACTION	99.6622
8-10	0.15	6	0.15	199	X-RAY DIFFRACTION	99.0338

Refinement TLS params.

Method: refined / Origin x: -14.9472 Å / Origin y: 4.3385 Å / Origin z: 3.6269 Å

	11	12	13	21	22	23	31	32	33
T	0.0845 Å²	-0.0532 Å²	-0.0065 Å²	-	0.0562 Å²	0.0049 Å²	-	-	0.0041 Å²
L	0.6906 °²	0.1655 °²	0.2631 °²	-	2.1463 °²	0.9089 °²	-	-	3.2453 °²
S	-0.1586 Å °	0.1593 Å °	-0.0009 Å °	-0.0391 Å °	0.1252 Å °	0.0146 Å °	-0.0054 Å °	0.2438 Å °	0.0334 Å °

Refinement TLS group

Selection: ALL

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi