PDB-8ojp: Human galectin 1 in complex with inhibitor

ID or keywords:

Entry

Database: PDB / ID: 8ojp

Title

Human galectin 1 in complex with inhibitor

Components

Galectin-1

Keywords

SUGAR BINDING PROTEIN / galectin / ligand / complex / sugar binding

Function / homology

Function and homology information

galectin complex / lactose binding / plasma cell differentiation / galactoside binding / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.71 Å

Authors

Hakansson, M. / Diehl, C. / Nilsson, U.J. / Zetterberg, F.R. / Peterson, K.

Funding support

1items

Citation

Journal: J.Med.Chem. / Year: 2023
Title: Discovery of Selective and Orally Available Galectin-1 Inhibitors.
Authors: Zetterberg, F.R. / Diehl, C. / Hakansson, M. / Kahl-Knutson, B. / Leffler, H. / Nilsson, U.J. / Peterson, K. / Roper, J.A. / Slack, R.J.

History

Deposition	Mar 24, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 12, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8ojp.cif.gz	288.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ojp.ent.gz	180.1 KB	Display	PDB format
PDBx/mmJSON format	8ojp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ojp_validation.pdf.gz	957.6 KB	Display	wwPDB validaton report
Full document	8ojp_full_validation.pdf.gz	963 KB	Display
Data in XML	8ojp_validation.xml.gz	16.2 KB	Display
Data in CIF	8ojp_validation.cif.gz	22.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/8ojp ftp://data.pdbj.org/pub/pdb/validation_reports/oj/8ojp	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-1

B: Galectin-1

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	53.350, 61.960, 100.730
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
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: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 3 - 133 / Label seq-ID: 4 - 134

Dom-ID
1
2

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

#1: Protein	Galectin-1 / Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L- ...Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / HBL / HPL / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / Putative MAPK-activating protein PM12 / S-Lac lectin 1 Mass: 14959.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09382
#2: Chemical	ChemComp-VPZ / (2~{R},3~{R},4~{S},5~{R},6~{R})-2-[3,5-bis(chloranyl)-4-fluoranyl-phenyl]sulfanyl-6-(hydroxymethyl)-4-[4-(1,3-thiazol-2-yl)-1,2,3-triazol-1-yl]oxane-3,5-diol Mass: 493.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₁₅Cl₂FN₄O₄S₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.78 Å³/Da / Density % sol: 55.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris pH 8, 28% PEG3350, 0.1 M Li2SO4, 1% beta-mercapthoethanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.918 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.918 Å / Relative weight: 1
Reflection	Resolution: 1.71→52.78 Å / Num. obs: 36768 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.041 / Net I/σ(I): 20.3
Reflection shell	Resolution: 1.71→1.74 Å / R_merge(I) obs: 0.672 / Num. unique obs: 2200 / CC_1/2: 0.842

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.71→52.775 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.958 / WR_factor R_free: 0.205 / WR_factor R_work: 0.164 / SU B: 4.623 / SU ML: 0.071 / Average fsc free: 0.9639 / Average fsc work: 0.9728 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.094
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2063	1863	5.067 %
R_work	0.1675	34905	-
all	0.169	-	-
obs	-	36768	99.799 %

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: 30.499 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.615 Å²	0 Å²	0 Å²
2-	-	2.583 Å²	-0 Å²
3-	-	-	-0.968 Å²

Refinement step

Cycle: LAST / Resolution: 1.71→52.775 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2058	0	66	222	2346

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	2233
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2057
X-RAY DIFFRACTION	r_angle_refined_deg	1.928	1.681	3036
X-RAY DIFFRACTION	r_angle_other_deg	0.637	1.591	4747
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.432	5	279
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.444	5	11
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.628	10	341
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.725	10	106
X-RAY DIFFRACTION	r_chiral_restr	0.325	0.2	327
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2656
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	528
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	303
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	1806
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	1045
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.09	0.2	1209
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.197	0.2	175
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.197	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.154	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.166	0.2	33
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.203	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	2.298	2.141	1088
X-RAY DIFFRACTION	r_mcbond_other	2.298	2.141	1088
X-RAY DIFFRACTION	r_mcangle_it	3.349	3.817	1363
X-RAY DIFFRACTION	r_mcangle_other	3.348	3.816	1364
X-RAY DIFFRACTION	r_scbond_it	3.757	2.596	1145
X-RAY DIFFRACTION	r_scbond_other	3.757	2.596	1145
X-RAY DIFFRACTION	r_scangle_it	5.641	4.548	1669
X-RAY DIFFRACTION	r_scangle_other	5.639	4.547	1670
X-RAY DIFFRACTION	r_lrange_it	7.758	24.352	2351
X-RAY DIFFRACTION	r_lrange_other	7.685	22.639	2296
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.098	0.05	4064

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	0.09804	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09804	0.05009

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
1.71-1.754	0.298	133	0.268	2548	0.27	2681	0.926	0.932	100	0.25
1.754-1.802	0.236	123	0.233	2478	0.233	2604	0.945	0.951	99.8848	0.202
1.802-1.855	0.259	117	0.225	2432	0.226	2553	0.929	0.953	99.8433	0.192
1.855-1.912	0.256	113	0.202	2357	0.204	2473	0.955	0.968	99.8787	0.164
1.912-1.974	0.204	138	0.186	2266	0.187	2406	0.971	0.974	99.9169	0.146
1.974-2.043	0.216	114	0.168	2206	0.17	2323	0.972	0.976	99.8709	0.133
2.043-2.12	0.197	118	0.171	2097	0.172	2218	0.968	0.977	99.8647	0.136
2.12-2.207	0.2	118	0.161	2067	0.163	2187	0.974	0.982	99.9085	0.13
2.207-2.305	0.185	114	0.153	1957	0.155	2075	0.968	0.982	99.8072	0.125
2.305-2.417	0.2	101	0.163	1895	0.165	2002	0.972	0.982	99.7003	0.138
2.417-2.548	0.203	99	0.159	1801	0.161	1900	0.972	0.983	100	0.137
2.548-2.702	0.19	94	0.154	1713	0.156	1810	0.978	0.984	99.8343	0.139
2.702-2.888	0.236	90	0.151	1588	0.155	1687	0.968	0.985	99.4665	0.141
2.888-3.118	0.208	91	0.166	1494	0.168	1591	0.974	0.983	99.6229	0.163
3.118-3.415	0.211	70	0.169	1398	0.171	1468	0.975	0.984	100	0.173
3.415-3.816	0.192	68	0.161	1272	0.163	1344	0.982	0.986	99.7024	0.174
3.816-4.402	0.139	48	0.128	1130	0.129	1189	0.989	0.99	99.0749	0.147
4.402-5.382	0.168	53	0.142	969	0.144	1026	0.983	0.99	99.6101	0.178
5.382-7.572	0.291	37	0.214	774	0.218	814	0.966	0.979	99.6315	0.243
7.572-52.775	0.319	24	0.222	463	0.226	491	0.956	0.966	99.1853	0.285

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.5513	0.4067	0.1943	1.3943	-0.1095	1.0959	-0.0638	0.0498	-0.0991	-0.0512	0.0072	-0.0853	0.0369	0.0795	0.0566	0.0266	0.0035	0.0132	0.0068	0.0025	0.0127	-29.3765	14.3632	-6.9488
2	1.3116	-0.0955	-0.4563	1.8003	0.3295	2.6107	0.0146	-0.1321	0.0568	0.1177	0.1479	0.0403	-0.0153	0.4451	-0.1624	0.0423	0.0103	0.0186	0.1291	-0.0554	0.0415	-9.0493	1.1444	-22.0285

Refinement TLS group

Selection: ALL

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