PDB-9uln: Mogamulizumab Fab fragment

ID or keywords:

Entry

Database: PDB / ID: 9uln

Title

Mogamulizumab Fab fragment

Components

anti-kappa VHH
heavy chain
light chain

Keywords

IMMUNE SYSTEM / mogamulizumab / CCR4 / antibody

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.94 Å

Authors

Heo, Y.-S.

Funding support

1items

Citation

Journal: To Be Published
Title: Structural insights into the therapeutic efficacy and resistance of mogamulizumab
Authors: Heo, Y.-S.

History

Deposition	Apr 20, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 22, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9uln.cif.gz	226.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9uln.ent.gz	183.1 KB	Display	PDB format
PDBx/mmJSON format	9uln.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/ul/9uln ftp://data.pdbj.org/pub/pdb/validation_reports/ul/9uln	HTTPS FTP

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Related structure data

Related structure data	9ullC 9ulmC C: citing same article (ref.)

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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)

Deposited unit

A: heavy chain

B: light chain

K: anti-kappa VHH

63.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	110.022, 110.022, 120.971
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Antibody	heavy chain Mass: 24809.686 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody	light chain Mass: 24117.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody	anti-kappa VHH Mass: 14365.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
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: 3.34 Å³/Da / Density % sol: 63.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.02M DL-Glutamic acid H2O, 0.02M DL-Alanine, 0.02M Glycine, 0.02M DL-Lysine monohydrochloride, 0.02M DL-Serine, 0.1M Sodium HEPES, MOPS(acid) pH 7.5, 12.5% v/v MPD, 12.5% PEG1000, 12.5% (W/V) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 2, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.94→50 Å / Num. obs: 18517 / % possible obs: 99.8 % / Redundancy: 9.6 % / CC_1/2: 0.983 / Net I/σ(I): 22.7
Reflection shell	Resolution: 2.94→3 Å / Num. unique obs: 925 / CC_1/2: 0.853

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Processing

Software

Name	Version	Classification
PHENIX	(1.20_4459: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
MOLREP		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.94→32.52 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.276	928	5.16 %
R_work	0.2231	-	-
obs	0.2258	17972	96.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.94→32.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4254	0	0	0	4254

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009
X-RAY DIFFRACTION	f_angle_d	1.292
X-RAY DIFFRACTION	f_dihedral_angle_d	8.128	605
X-RAY DIFFRACTION	f_chiral_restr	0.063	651
X-RAY DIFFRACTION	f_plane_restr	0.012	764

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 (%)
2.94-3.09	0.513	129	0.3757	2452	X-RAY DIFFRACTION	98
3.09-3.28	0.3794	114	0.3173	2430	X-RAY DIFFRACTION	98
3.28-3.54	0.3553	167	0.2887	2408	X-RAY DIFFRACTION	98
3.54-3.89	0.3598	101	0.2713	2393	X-RAY DIFFRACTION	96
3.89-4.45	0.2923	124	0.2133	2340	X-RAY DIFFRACTION	94
4.45-5.61	0.2281	149	0.188	2432	X-RAY DIFFRACTION	96
5.61-32.52	0.1929	144	0.1675	2589	X-RAY DIFFRACTION	98

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	3.7135	-1.0143	0.1298	4.0304	0.6	3.5855	-0.4867	0.2954	-0.757	0.9636	0.991	0.3211	-0.2837	0.1886	-0.402	0.9748	-0.0501	0.1074	0.5747	0.0913	0.8345	20.9493	16.0906	23.0314
2	3.0146	-0.4104	0.5906	3.3771	-1.8087	1.75	-0.2311	-0.079	-0.7039	0.9244	0.1823	0.6985	0.1695	-0.5468	-0.1342	0.7747	0.1048	0.2794	0.7096	0.1258	0.9593	13.2335	24.7275	22.3995
3	1.6901	-1.2445	-0.3895	4.2126	0.4239	1.1508	-0.3367	-0.1169	-0.5793	0.4093	0.0807	1.0587	0.0796	0.012	0.3547	0.6267	0.0526	0.0945	0.5766	0.0706	0.7675	21.3172	21.5348	18.2082
4	2.8533	0.6984	0.9516	2.552	1.0373	3.0094	-0.1667	-0.0302	-0.1291	0.4362	0.2637	0.2518	0.6882	0.3423	-0.0662	0.6601	0.0733	0.0389	0.4808	0.0553	0.5431	47.9848	10.7098	16.0086
5	0.9103	-1.154	0.01	1.4273	0.1008	1.4014	0.5919	-0.4549	0.2309	-0.0715	-0.5275	-0.324	-0.0042	-0.225	0.0427	0.5683	0.1292	-0.0059	0.6485	0.107	0.6726	32.3639	39.9405	6.7466
6	2.4185	-1.3616	-0.9359	1.0701	0.3943	1.2715	0.7633	0.0642	0.0712	-0.1964	-0.4952	0.1036	-0.2869	-0.4627	0.0592	0.6472	0.1578	-0.0404	0.8065	-0.0442	0.5911	16.7949	44.4251	9.2502
7	3.0853	0.8959	0.0123	2.6279	-0.4637	1.1889	0.033	-0.2092	0.1122	0.4108	-0.0735	0.2419	-0.5815	-0.1021	0.0214	0.6039	0.2079	0.0215	0.6071	0.0324	0.533	27.3118	42.4908	17.1529
8	5.6152	-0.1198	-1.2505	2.9027	-0.148	1.8172	0.2738	-0.7336	-0.4359	0.2017	-0.4564	-0.3482	-0.0199	0.4508	0.3257	0.5903	0.0795	0.0327	0.8818	0.0195	0.4146	33.1521	39.3154	15.3444
9	1.3869	-1.1832	-1.0276	1.5123	0.426	0.8483	-0.0292	-0.0552	0.4654	0.1528	0.1632	0.0801	-0.0398	-0.2814	-0.105	0.5048	0.1192	-0.0156	0.7495	-0.05	0.5747	32.3431	34.9295	8.9669
10	3.4489	-0.1855	-0.9537	2.9561	0.6032	2.4441	-0.4482	0.3761	-0.7497	1.0012	0.7656	-0.7881	0.97	0.216	0.4455	0.8534	0.2225	0.0906	0.5999	0.0826	0.5708	51.9322	5.269	6.0525
11	1.25	-1.0258	-1.121	3.8169	0.7421	1.7395	0.1417	0.0626	-0.0777	0.6741	-0.2527	-0.2817	0.2906	-0.3989	0.1168	0.6866	0.0017	-0.0496	0.5623	-0.0435	0.4993	48.8427	19.3092	1.1171
12	0.2131	-0.3407	-0.6832	0.8017	1.2879	2.4881	0.0432	0.1708	-0.4177	-0.3541	0.0453	0.3505	-0.2211	-0.2521	-0.067	0.7135	0.0864	-0.0879	0.8096	0.0133	0.6533	45.264	12.9575	-4.8594
13	1.2182	-0.2945	0.5076	2.616	0.8819	1.634	-0.177	-0.1181	-0.1566	-0.0691	0.1058	0.5426	0.0498	-0.0326	0.015	0.5647	0.0242	0.0194	0.5459	0.0671	0.5792	49.1144	14.9967	2.0051
14	3.0544	0.9278	0.4529	8.2847	2.4828	2.2084	0.2617	0.1141	-0.4976	0.7301	-0.5479	-1.7712	0.5637	0.1494	-0.1073	0.6249	0.1705	-0.0226	0.6234	0.0066	0.5378	57.9999	15.3428	-2.6964
15	9.3028	2.2629	8.9552	2.1443	1.8391	8.8667	0.2751	1.3548	-0.1734	-0.4632	0.728	0.8576	-0.5008	0.8198	-0.4456	1.2209	0.0644	0.0926	0.7113	-0.0245	0.6244	54.4005	40.2297	-19.385
16	2.7224	-0.0376	-1.4818	1.6679	-0.4681	4.8271	-0.4799	0.9882	0.1479	-0.4394	0.7607	0.1134	-1.9705	0.581	-0.3562	1.1267	-0.086	0.0604	0.6608	-0.0098	0.6695	54.9543	47.2369	-11.4856
17	4.6897	1.7022	0.6826	2.4237	0.0571	3.3135	-0.0422	-0.6438	-0.3287	0.3369	-0.0522	0.0303	-0.5038	-0.1964	0.1081	0.7185	0.1351	0.0446	0.5387	0.0051	0.5668	55.536	39.182	-2.9972
18	2.0859	-0.0188	-2.0671	2.982	0.332	2.0268	0.214	0.1967	0.2595	0.1528	0.1274	0.0164	-0.5738	0.2202	-0.4451	0.8916	-0.001	-0.0278	0.61	0.018	0.5573	55.8785	42.7982	-7.7731

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 83 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 84 through 125 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 126 through 222 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 18 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 19 through 37 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 38 through 80 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 81 through 95 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 96 through 118 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 119 through 133 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 134 through 155 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 156 through 168 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 169 through 203 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 204 through 219 )
15	X-RAY DIFFRACTION	15	chain 'K' and (resid 1 through 7 )
16	X-RAY DIFFRACTION	16	chain 'K' and (resid 8 through 32 )
17	X-RAY DIFFRACTION	17	chain 'K' and (resid 33 through 65 )
18	X-RAY DIFFRACTION	18	chain 'K' and (resid 66 through 121 )

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