PDB-9fxz: Galectin-8 N-terminal carbohydrate recognition domain in complex ...

ID or keywords:

Entry

Database: PDB / ID: 9fxz

Title

Galectin-8 N-terminal carbohydrate recognition domain in complex with 4-(bromophenyl)phthalazinone D-galactal ligand

Components

Galectin-8

Keywords

IMMUNE SYSTEM / Galectin / phthalazinone / inhibitor / sugar binding protein

Function / homology

Function and homology information

lymphatic endothelial cell migration / xenophagy / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / extracellular space / membrane / cytosol / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.3 Å

Authors

Van Klaveren, S. / Hakansson, M. / Diehl, C. / Nilsson, N.J.

Funding support

European Union, 1items

Citation

Journal: Acs Med.Chem.Lett. / Year: 2024
Title: Galectin-8N-Selective 4-Halophenylphthalazinone-Galactals Double pi-Stack in a Unique Pocket.
Authors: van Klaveren, S. / Hassan, M. / Hakansson, M. / Johnsson, R.E. / Larsson, J. / Jakopin, Z. / Anderluh, M. / Leffler, H. / Tomasic, T. / Nilsson, U.J.

History

Deposition	Jul 2, 2024	Deposition site: PDBE / Processing site: PDBE
Supersession	Jul 16, 2025	ID: 8CM8
Revision 1.0	Jul 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9fxz.cif.gz	330.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9fxz.ent.gz	219 KB	Display	PDB format
PDBx/mmJSON format	9fxz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9fxz_validation.pdf.gz	734.2 KB	Display	wwPDB validaton report
Full document	9fxz_full_validation.pdf.gz	736.3 KB	Display
Data in XML	9fxz_validation.xml.gz	19.5 KB	Display
Data in CIF	9fxz_validation.cif.gz	27.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fx/9fxz ftp://data.pdbj.org/pub/pdb/validation_reports/fx/9fxz	HTTPS FTP

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Related structure data

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

Deposited unit

A: Galectin-8

B: Galectin-8

hetero molecules

72.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Galectin-8

hetero molecules

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

2

B: Galectin-8

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.71, 62.28, 84.75
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: PHE / End label comp-ID: PHE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 8 - 153 / Label seq-ID: 8 - 153

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Galectin-8 / Gal-8 / Po66 carbohydrate-binding protein / Po66-CBP / Prostate carcinoma tumor antigen 1 / PCTA-1 Mass: 35854.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214
#2: Chemical	ChemComp-V19 / 4-(4-bromophenyl)-2-[[(2~{R},3~{R},4~{R})-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2~{H}-pyran-4-yl]oxymethyl]phthalazin-1-one Mass: 459.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₁₉BrN₂O₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.17 Å³/Da / Density % sol: 43.38 %
Crystal grow	Temperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 8 Details: A co-crystal with lactose, grown from 12 mg/ml galectin-8N in 10 mM lactose, 10 mM Tris/HCl pH 8.0, 1 mM TCEP and 150 mM sodium chloride mixed with 25% (w/v) PEG 2000 MME) in a hanging drop, ...Details: A co-crystal with lactose, grown from 12 mg/ml galectin-8N in 10 mM lactose, 10 mM Tris/HCl pH 8.0, 1 mM TCEP and 150 mM sodium chloride mixed with 25% (w/v) PEG 2000 MME) in a hanging drop, was used to soak the compound by transferring crystals in three steps to soaking drops. These were 2 uL drops with a soaking solution of 20% ethylene glycol, 25% PEG 2000 MME, 10 mM Tris pH 8, 1 mM TCEP, 50 mM NaCl, and 2 mM compound 10. The incubation times in the first two drops were about 10 min and in the third drop about 24 h. Then the crystals were transferred to a cryo solution with the same constituents and flash-frozen in liquid nitrogen.

Crystal

Density Matthews: 2.17 Å³/Da / Density % sol: 43.38 %

Crystal grow

Temperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 8
Details: A co-crystal with lactose, grown from 12 mg/ml galectin-8N in 10 mM lactose, 10 mM Tris/HCl pH 8.0, 1 mM TCEP and 150 mM sodium chloride mixed with 25% (w/v) PEG 2000 MME) in a hanging drop, ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Sep 18, 2021 Details: Oxford Danfysik/SESO Two stage demagnification using two K-B pairs of bimorph type mirrors
Radiation	Monochromator: ACCEL Fixed exit Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 1.3→46.01 Å / Num. obs: 71690 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC_1/2: 0.998 / Net I/σ(I): 12.5
Reflection shell	Resolution: 1.3→1.32 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3466 / CC_1/2: 0.593 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
xia2	0.3.6.3	data reduction
Aimless	0.7.7	data scaling
PHASER	2.7.14	phasing
Coot	0.9.8.1	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.3→46.007 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.965 / SU B: 2.238 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2003	3642	5.08 %
R_work	0.1572	68048	-
all	0.159	-	-
obs	-	71690	99.729 %

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: 23.87 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.476 Å²	-0 Å²	-0 Å²
2-	-	0.253 Å²	-0 Å²
3-	-	-	-0.729 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→46.007 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2352	0	59	288	2699

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	2593
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2494
X-RAY DIFFRACTION	r_angle_refined_deg	1.793	1.848	3530
X-RAY DIFFRACTION	r_angle_other_deg	0.634	1.795	5738
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.336	5	322
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.44	5	18
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.769	10	447
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.743	10	119
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	381
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	3068
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	634
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	373
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.2	0.2	2175
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	1215
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1302
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	160
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.253	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.209	0.2	57
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.152	0.2	24
X-RAY DIFFRACTION	r_mcbond_it	7.287	2.099	1230
X-RAY DIFFRACTION	r_mcbond_other	7.244	2.097	1229
X-RAY DIFFRACTION	r_mcangle_it	9.127	3.773	1548
X-RAY DIFFRACTION	r_mcangle_other	9.138	3.773	1548
X-RAY DIFFRACTION	r_scbond_it	9.07	2.468	1363
X-RAY DIFFRACTION	r_scbond_other	9.066	2.469	1364
X-RAY DIFFRACTION	r_scangle_it	11.92	4.395	1974
X-RAY DIFFRACTION	r_scangle_other	11.917	4.394	1975
X-RAY DIFFRACTION	r_lrange_it	18.332	29.639	13057
X-RAY DIFFRACTION	r_lrange_other	18.132	29.571	12937
X-RAY DIFFRACTION	r_rigid_bond_restr	5.218	3	5087
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.124	0.05	4552

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.12359	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.12359	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.3-1.334	0.302	290	0.279	4942	0.28	5244	0.936	0.947	99.7712	0.276
1.334-1.37	0.294	252	0.245	4856	0.248	5109	0.944	0.961	99.9804	0.238
1.37-1.41	0.265	245	0.218	4716	0.22	4961	0.956	0.969	100	0.207
1.41-1.453	0.236	233	0.184	4611	0.187	4845	0.961	0.979	99.9794	0.167
1.453-1.501	0.209	231	0.161	4466	0.163	4698	0.971	0.984	99.9787	0.143
1.501-1.554	0.224	240	0.152	4300	0.156	4543	0.965	0.985	99.934	0.134
1.554-1.612	0.207	204	0.14	4172	0.143	4376	0.973	0.988	100	0.122
1.612-1.678	0.167	216	0.116	4015	0.119	4231	0.982	0.991	100	0.104
1.678-1.752	0.198	211	0.12	3857	0.123	4069	0.977	0.991	99.9754	0.108
1.752-1.838	0.182	198	0.124	3702	0.127	3901	0.98	0.99	99.9744	0.117
1.838-1.937	0.22	201	0.156	3454	0.16	3719	0.969	0.984	98.2791	0.15
1.937-2.054	0.208	183	0.136	3313	0.139	3496	0.975	0.989	100	0.139
2.054-2.196	0.189	186	0.136	3157	0.139	3346	0.977	0.989	99.9103	0.146
2.196-2.371	0.174	135	0.148	2925	0.149	3082	0.981	0.986	99.2862	0.162
2.371-2.597	0.193	173	0.15	2679	0.152	2855	0.977	0.986	99.8949	0.172
2.597-2.902	0.226	119	0.162	2469	0.165	2594	0.968	0.984	99.7687	0.191
2.902-3.349	0.176	102	0.16	2192	0.161	2304	0.98	0.984	99.566	0.198
3.349-4.096	0.194	99	0.16	1873	0.162	1986	0.98	0.984	99.2951	0.198
4.096-5.77	0.179	78	0.155	1468	0.156	1561	0.982	0.987	99.0391	0.224
5.77-46.007	0.225	46	0.202	881	0.203	939	0.97	0.972	98.722	0.282

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