PDB-9i9h: Structure of FAB-fragment GB11 in complex with Sialyl Lewis A

ID or keywords:

Entry

Database: PDB / ID: 9i9h

Title

Structure of FAB-fragment GB11 in complex with Sialyl Lewis A

Components

(IgG antibody ...) x 2

Keywords

IMMUNE SYSTEM / Fab fragment / Carbohydrate / complex

Function / homology

beta-D-galactopyranose / DI(HYDROXYETHYL)ETHER / N-acetyl-alpha-neuraminic acid

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.96 Å

Authors

Freitag, A. / Khan-Kilji, S. / Nedielkov, R. / Murali Kumar, S. / Krummhaar, M. / Luehle, J. / Goerdeler, F. / Arndt, J. / Kamphues, C. / Mroginski, M.A. ...

Funding support

Germany, 1items

Citation

Journal: Jacs Au / Year: 2026
Title: Integrative Approach to Develop and Characterize Antibodies against the Cancer-Associated Antigen Sialyl Lewis A (CA 19-9).
Authors: Freitag, A. / Khilji, S.K. / Nedielkov, R. / M Kumar, S. / Krummhaar, M. / Arndt, J. / Moreira, G.M.S.G. / Luhle, J. / Goerdeler, F. / Kamphues, C. / Mroginski, M.A. / Roth, C. / Seeberger, ...

History

Deposition	Feb 6, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 18, 2026	Provider: repository / Type: Initial release
Revision 1.1	May 13, 2026	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9i9h.cif.gz	610.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9i9h.ent.gz	515.8 KB	Display	PDB format
PDBx/mmJSON format	9i9h.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/i9/9i9h ftp://data.pdbj.org/pub/pdb/validation_reports/i9/9i9h	HTTPS FTP

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Related structure data

Related structure data	9i6qC 916q C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #113 - May 2009 Influenza Neuraminidase similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1)

Deposited unit

A: IgG antibody FAB fragment

B: IgG antibody Fab fragment

L: IgG antibody Fab fragment

D: IgG antibody Fab fragment

F: IgG antibody Fab fragment

H: IgG antibody FAB fragment

C: IgG antibody FAB fragment

E: IgG antibody FAB fragment

hetero molecules

192 kDa, 8 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)	39.838, 108.697, 108.920
Angle α, β, γ (deg.)	89.602, 87.339, 89.251
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	CYS	CYS	1 - 217	1 - 217
2	1	1	CYS	CYS	1 - 217	1 - 217
3	2	2	CYS	CYS	1 - 217	1 - 217
4	2	2	CYS	CYS	1 - 217	1 - 217
5	3	3	CYS	CYS	1 - 217	1 - 217
6	3	3	CYS	CYS	1 - 217	1 - 217
7	4	4	ILE	ILE	1 - 212	1 - 212
8	4	4	ILE	ILE	1 - 212	1 - 212
9	5	5	ILE	ILE	1 - 212	1 - 212
10	5	5	ILE	ILE	1 - 212	1 - 212
11	6	6	ILE	ILE	1 - 212	1 - 212
12	6	6	ILE	ILE	1 - 212	1 - 212
13	7	7	ILE	ILE	1 - 212	1 - 212
14	7	7	ILE	ILE	1 - 212	1 - 212
15	8	8	ILE	ILE	1 - 212	1 - 212
16	8	8	ILE	ILE	1 - 212	1 - 212
17	9	9	ILE	ILE	1 - 212	1 - 212
18	9	9	ILE	ILE	1 - 212	1 - 212
19	10	10	CYS	CYS	1 - 217	1 - 217
20	10	10	CYS	CYS	1 - 217	1 - 217
21	11	11	CYS	CYS	1 - 217	1 - 217
22	11	11	CYS	CYS	1 - 217	1 - 217
23	12	12	CYS	CYS	1 - 217	1 - 217
24	12	12	CYS	CYS	1 - 217	1 - 217

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24

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Antibody , 2 types, 8 molecules AHCEBLDF

#1: Antibody	IgG antibody FAB fragment Mass: 23304.133 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: heavy chain / Source: (natural) Mus musculus (house mouse) / Organ: spleen
#2: Antibody	IgG antibody Fab fragment Mass: 23742.287 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: light chain / Source: (natural) Mus musculus (house mouse) / Tissue: spleen

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Sugars , 5 types, 8 molecules

#3: Polysaccharide

beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGalpb1-3[LFucpa1-4]DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_a4-c1	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}[(4+1)][a-L-Fucp]{}}	LINUCS	PDB-CARE

#4: Polysaccharide

N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2- ...

Type: oligosaccharide / Mass: 820.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DNeup5Aca2-3DGalpb1-3[LFucpa1-4]DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5NCC/3=O][a1221m-1a_1-5]/1-2-3-4/a3-b1_a4-d1_b3-c2	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}[(4+1)][a-L-Fucp]{}}	LINUCS	PDB-CARE

#5: Polysaccharide

alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
LFucpa1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a4-b1	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][a-L-Fucp]{}}	LINUCS	PDB-CARE

#6: Sugar

ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID

Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₁H₁₉NO₉ / Feature type: SUBJECT OF INVESTIGATION

Identifier	Type	Program
DNeup5Aca	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-a-D-neuraminic acid	COMMON NAME	GMML 1.0
a-D-Neup5Ac	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Neu5Ac	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#8: Sugar

ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 2 types, 23 molecules

#7: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₃ / Feature type: SUBJECT OF INVESTIGATION
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	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: 2.51 Å³/Da / Density % sol: 51.1 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: sodium malonate PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 10, 2021
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.9→26.98 Å / Num. obs: 40947 / % possible obs: 98.2 % / Redundancy: 3 % / B_iso Wilson estimate: 49.14 Å² / CC_1/2: 0.915 / R_pim(I) all: 0.222 / R_rim(I) all: 0.407 / Net I/σ(I): 2.8
Reflection shell	Resolution: 2.9→3.02 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4497 / CC_1/2: 0.189 / R_pim(I) all: 1.359 / R_rim(I) all: 2.583

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.96→26.696 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.884 / Cross valid method: FREE R-VALUE / ESU R Free: 0.462
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2479	1994	5.306 %
R_work	0.2097	35589	-
all	0.212	-	-
obs	-	37583	98.697 %

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: 61.588 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.256 Å²	-1.535 Å²	0.416 Å²
2-	-	0.204 Å²	0.366 Å²
3-	-	-	-2.447 Å²

Refinement step

Cycle: LAST / Resolution: 2.96→26.696 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13216	0	259	18	13493

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	13817
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	12434
X-RAY DIFFRACTION	r_ext_dist_refined_b	0.01	0.015	11
X-RAY DIFFRACTION	r_angle_refined_deg	1.321	1.812	18784
X-RAY DIFFRACTION	r_angle_other_deg	0.741	1.743	28862
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.814	5	1710
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.989	5	64
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.574	10	2173
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	12.744	10	557
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	2105
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	15989
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	3087
X-RAY DIFFRACTION	r_nbd_refined	0.252	0.2	2495
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.232	0.2	11926
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	6660
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	7079
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.259	0.2	341
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.075	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.212	0.2	43
X-RAY DIFFRACTION	r_nbd_other	0.271	0.2	236
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.341	0.2	12
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.132	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	5.303	6.096	6861
X-RAY DIFFRACTION	r_mcbond_other	5.302	6.096	6861
X-RAY DIFFRACTION	r_mcangle_it	8.594	10.944	8564
X-RAY DIFFRACTION	r_mcangle_other	8.594	10.945	8565
X-RAY DIFFRACTION	r_scbond_it	5.015	6.414	6956
X-RAY DIFFRACTION	r_scbond_other	5.015	6.414	6957
X-RAY DIFFRACTION	r_scangle_it	8.284	11.641	10220
X-RAY DIFFRACTION	r_scangle_other	8.284	11.641	10221
X-RAY DIFFRACTION	r_lrange_it	13.77	74.262	55895
X-RAY DIFFRACTION	r_lrange_other	13.77	74.262	55896
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.098	0.05	6577
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.099	0.05	6577
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.15	0.05	6239
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.085	0.05	6621
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.088	0.05	6581
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.083	0.05	6587
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.088	0.05	6605
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.091	0.05	6604
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.096	0.05	6565
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.088	0.05	6603
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.148	0.05	6249
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.148	0.05	6222

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	0.0978	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.0978	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09905	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.09905	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.15	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.15	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.0853	0.05011
4	8	A	X-RAY DIFFRACTION	Local ncs	0.0853	0.05011
5	9	A	X-RAY DIFFRACTION	Local ncs	0.08808	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.08808	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.08269	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.08269	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.08838	0.05011
7	14	A	X-RAY DIFFRACTION	Local ncs	0.08838	0.05011
8	15	A	X-RAY DIFFRACTION	Local ncs	0.09102	0.05011
8	16	A	X-RAY DIFFRACTION	Local ncs	0.09102	0.05011
9	17	A	X-RAY DIFFRACTION	Local ncs	0.0955	0.05011
9	18	A	X-RAY DIFFRACTION	Local ncs	0.0955	0.05011
10	19	A	X-RAY DIFFRACTION	Local ncs	0.08751	0.05011
10	20	A	X-RAY DIFFRACTION	Local ncs	0.08751	0.05011
11	21	A	X-RAY DIFFRACTION	Local ncs	0.14811	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.14811	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.14764	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.14764	0.0501

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
2.96-3.036	0.362	145	0.354	2657	0.355	2849	0.899	0.908	98.3503	0.356
3.036-3.118	0.341	134	0.348	2516	0.348	2691	0.91	0.907	98.4764	0.352
3.118-3.207	0.33	98	0.326	2483	0.326	2613	0.917	0.919	98.7754	0.329
3.207-3.304	0.317	114	0.319	2443	0.319	2624	0.929	0.925	97.4466	0.319
3.304-3.411	0.352	117	0.283	2268	0.287	2423	0.908	0.943	98.4317	0.281
3.411-3.529	0.278	135	0.241	2247	0.243	2402	0.947	0.959	99.1674	0.235
3.529-3.659	0.272	121	0.232	2210	0.234	2358	0.949	0.962	98.855	0.222
3.659-3.806	0.226	121	0.197	2054	0.198	2199	0.966	0.974	98.9086	0.185
3.806-3.971	0.242	120	0.208	2067	0.21	2204	0.956	0.971	99.2287	0.196
3.971-4.161	0.212	94	0.177	1895	0.178	2010	0.969	0.98	98.9552	0.162
4.161-4.38	0.246	92	0.166	1883	0.17	1993	0.961	0.982	99.0968	0.151
4.38-4.638	0.177	118	0.138	1660	0.14	1800	0.983	0.988	98.7778	0.123
4.638-4.947	0.192	79	0.133	1698	0.135	1792	0.98	0.989	99.1629	0.118
4.947-5.328	0.239	136	0.143	1441	0.151	1590	0.971	0.988	99.1824	0.124
5.328-5.814	0.217	104	0.155	1403	0.159	1514	0.969	0.986	99.5376	0.139
5.814-6.462	0.217	52	0.165	1299	0.167	1365	0.973	0.983	98.9744	0.145
6.462-7.39	0.225	70	0.178	1115	0.181	1196	0.967	0.98	99.0803	0.162
7.39-8.882	0.216	78	0.156	955	0.16	1039	0.973	0.986	99.4225	0.143
8.882-11.919	0.188	22	0.163	803	0.164	828	0.977	0.987	99.6377	0.159
11.919-26.696	0.253	44	0.307	491	0.302	537	0.963	0.949	99.6276	0.302

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Antibody , 2 types, 8 molecules AHCEBLDF

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Sugars , 5 types, 8 molecules

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Non-polymers , 2 types, 23 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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About Yorodumi

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-Antibody , 2 types, 8 molecules AHCEBLDF

-Sugars , 5 types, 8 molecules

-Non-polymers , 2 types, 23 molecules

-Details

-Experimental details

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Antibody , 2 types, 8 molecules AHCEBLDF

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Sugars , 5 types, 8 molecules

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Non-polymers , 2 types, 23 molecules

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