PDB-9wnx: beta-lactoglobulin in complex with Perfluorooctanesulfonic acid (PFOS)

ID or keywords:

Entry

Database: PDB / ID: 9wnx

Title

beta-lactoglobulin in complex with Perfluorooctanesulfonic acid (PFOS)

Components

Beta-lactoglobulin

Keywords

LIPID BINDING PROTEIN / beta-lactoglobulin / Perfluorooctanesulfonic acid (PFOS)

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: 2.5 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

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Download

PDBx/mmCIF format	9wnx.cif.gz	95.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9wnx.ent.gz	60.6 KB	Display	PDB format
PDBx/mmJSON format	9wnx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (5) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: Beta-lactoglobulin

hetero molecules

18.9 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)	53.36, 53.36, 110.197
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 Details: beta-lactoglobulin in complex with Perfluorooctanesulfonic acid (PFOS) Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02754
#2: Chemical	ChemComp-P8S / heptadecafluoro-1-octanesulfonic acid / perfluorooctane sulfonate Mass: 500.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈HF₁₇O₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.477 Å³/Da / Density % sol: 50.38 % / 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

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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: Jan 5, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54184 Å / Relative weight: 1
Reflection	Resolution: 2.5→28.75 Å / Num. obs: 6720 / % possible obs: 99.9 % / Redundancy: 18.83 % / R_merge(I) obs: 0.159 / Net I/σ(I): 14.6
Reflection shell	Resolution: 2.5→2.6 Å / Redundancy: 13.84 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 742 / CC_1/2: 0.538 / % possible all: 100

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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: 2.5→23.116 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.9 / SU B: 25.143 / SU ML: 0.248 / Cross valid method: FREE R-VALUE / ESU R: 0.552 / ESU R Free: 0.304 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2613	343	5.127 %
R_work	0.1946	6347	-
all	0.198	-	-
obs	-	6690	99.776 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 66.611 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.177 Å²	-0.089 Å²	0 Å²
2-	-	-0.177 Å²	0 Å²
3-	-	-	0.575 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→23.116 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1258	0	30	9	1297

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	1332
X-RAY DIFFRACTION	r_angle_refined_deg	2.107	1.847	1821
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.196	5	163
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.288	5	3
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.648	10	255
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.343	10	55
X-RAY DIFFRACTION	r_chiral_restr	0.146	0.2	216
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	960
X-RAY DIFFRACTION	r_nbd_refined	0.255	0.2	529
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	852
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.197	0.2	54
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.279	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.113	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	5.888	4.66	649
X-RAY DIFFRACTION	r_mcangle_it	9.15	8.339	813
X-RAY DIFFRACTION	r_scbond_it	7.952	5.218	683
X-RAY DIFFRACTION	r_scangle_it	11.879	9.346	1008
X-RAY DIFFRACTION	r_lrange_it	16.334	49.315	1857

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 (%)
2.5-2.564	0.362	40	0.28	444	X-RAY DIFFRACTION	100
2.564-2.634	0.374	20	0.288	439	X-RAY DIFFRACTION	100
2.634-2.709	0.354	25	0.244	436	X-RAY DIFFRACTION	100
2.709-2.791	0.246	19	0.245	413	X-RAY DIFFRACTION	100
2.791-2.881	0.297	18	0.251	413	X-RAY DIFFRACTION	100
2.881-2.981	0.288	28	0.221	394	X-RAY DIFFRACTION	100
2.981-3.091	0.275	24	0.237	366	X-RAY DIFFRACTION	100
3.091-3.215	0.375	14	0.22	379	X-RAY DIFFRACTION	100
3.215-3.355	0.294	14	0.218	366	X-RAY DIFFRACTION	100
3.355-3.515	0.376	18	0.203	336	X-RAY DIFFRACTION	99.7183
3.515-3.701	0.212	27	0.156	318	X-RAY DIFFRACTION	100
3.701-3.919	0.285	8	0.149	311	X-RAY DIFFRACTION	100
3.919-4.181	0.136	16	0.136	299	X-RAY DIFFRACTION	100
4.181-4.504	0.222	14	0.144	277	X-RAY DIFFRACTION	100
4.504-4.915	0.148	12	0.124	255	X-RAY DIFFRACTION	100
4.915-5.464	0.263	9	0.169	240	X-RAY DIFFRACTION	100
5.464-6.252	0.3	20	0.208	203	X-RAY DIFFRACTION	100
6.252-7.52	0.235	10	0.197	188	X-RAY DIFFRACTION	100
7.52-10	0.22	5	0.173	159	X-RAY DIFFRACTION	100
8-10	0.12	2	0.12	111	X-RAY DIFFRACTION	99.1228

Refinement TLS params.

Method: refined / Origin x: 14.8967 Å / Origin y: -4.5354 Å / Origin z: 3.4895 Å

	11	12	13	21	22	23	31	32	33
T	0.2819 Å²	-0.1162 Å²	-0.0101 Å²	-	0.1384 Å²	0.0011 Å²	-	-	0.0353 Å²
L	0.1837 °²	0.1273 °²	-0.2411 °²	-	1.2748 °²	-0.6368 °²	-	-	2.5561 °²
S	-0.2116 Å °	0.1293 Å °	0.0112 Å °	-0.0231 Å °	0.1951 Å °	-0.1612 Å °	0.114 Å °	-0.3048 Å °	0.0165 Å °

Refinement TLS group

Selection: ALL

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