PDB-9n7m: Designed anti-OSM Fab

ID or keywords:

Entry

Database: PDB / ID: 9n7m

Title

Designed anti-OSM Fab

Components

Designed Fab light chain
designed Fab heavy chain

Keywords

IMMUNE SYSTEM / machine learning / antibody / design

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Kiefer, J.R. / Alberstein, R.G. / Hofmann, J.L. / Watkins, A.M. / Seeger, F. / Dou, Y. / Zhang, X.

Funding support

1items

Citation

Journal: To Be Published
Title: Lab-in-the-loop therapeutic antibody design with deep learning
Authors: Frey, N.C. / Hofmann, J.L. / Kiefer, J.R. / Alberstein, R.G. / Seeger, F. / Watkins, A.M. / Bonneau, R.

History

Deposition	Feb 6, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 11, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9n7m.cif.gz	358.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9n7m.ent.gz	292 KB	Display	PDB format
PDBx/mmJSON format	9n7m.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/n7/9n7m ftp://data.pdbj.org/pub/pdb/validation_reports/n7/9n7m	HTTPS FTP

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Related structure data

Related structure data	9n2vC 9n7oC 9muy PDB Unreleased entry 9muz PDB Unreleased entry 9mvj PDB Unreleased entry 9mzc PDB Unreleased entry 9mzv PDB Unreleased entry 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

H: designed Fab heavy chain

L: Designed Fab light chain

A: designed Fab heavy chain

B: Designed Fab light chain

hetero molecules

95.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

H: designed Fab heavy chain

L: Designed Fab light chain

hetero molecules

defined by author&software
Evidence: gel filtration
47.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: designed Fab heavy chain

B: Designed Fab light chain

hetero molecules

defined by author&software
Evidence: gel filtration
47.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	116.836, 116.836, 101.458
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

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Antibody , 2 types, 4 molecules HALB

#1: Antibody	designed Fab heavy chain Mass: 24376.189 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	Designed Fab light chain Mass: 23127.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 4 types, 837 molecules

#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 826 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 3.64 Å³/Da / Density % sol: 66.25 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, 30% w/v PEG5000 MME

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Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 12, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.15→46.53 Å / Num. obs: 74105 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC_1/2: 0.984 / R_merge(I) obs: 0.224 / R_pim(I) all: 0.111 / R_rim(I) all: 0.251 / Χ²: 0.93 / Net I/σ(I): 7.7 / Num. measured all: 375920
Reflection shell	Resolution: 2.15→2.2 Å / % possible obs: 100 % / Redundancy: 4.2 % / R_merge(I) obs: 0.707 / Num. measured all: 19268 / Num. unique obs: 4549 / CC_1/2: 0.154 / R_pim(I) all: 0.39 / R_rim(I) all: 0.81 / Χ²: 0.84 / Net I/σ(I) obs: 2

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.2_5419: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.15→41.31 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2419	3682	4.98 %
R_work	0.2096	-	-
obs	0.2113	73985	99.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.15→41.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6570	0	40	826	7436

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6792
X-RAY DIFFRACTION	f_angle_d	0.512	9244
X-RAY DIFFRACTION	f_dihedral_angle_d	11.445	2413
X-RAY DIFFRACTION	f_chiral_restr	0.043	1033
X-RAY DIFFRACTION	f_plane_restr	0.004	1187

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 (%)
2.15-2.18	0.3799	139	0.3313	2729	X-RAY DIFFRACTION	100
2.18-2.21	0.3144	128	0.3169	2693	X-RAY DIFFRACTION	100
2.21-2.24	0.3638	140	0.3087	2707	X-RAY DIFFRACTION	100
2.24-2.27	0.3344	142	0.3174	2661	X-RAY DIFFRACTION	100
2.27-2.31	0.3235	129	0.3012	2725	X-RAY DIFFRACTION	100
2.31-2.35	0.3255	121	0.2966	2710	X-RAY DIFFRACTION	100
2.35-2.39	0.3513	139	0.2925	2699	X-RAY DIFFRACTION	100
2.39-2.43	0.3182	152	0.2893	2685	X-RAY DIFFRACTION	100
2.43-2.48	0.3214	129	0.2632	2707	X-RAY DIFFRACTION	100
2.48-2.53	0.2699	141	0.2641	2702	X-RAY DIFFRACTION	100
2.53-2.58	0.2757	145	0.2527	2707	X-RAY DIFFRACTION	100
2.58-2.64	0.2837	129	0.2458	2692	X-RAY DIFFRACTION	100
2.64-2.71	0.2905	139	0.2359	2707	X-RAY DIFFRACTION	100
2.71-2.78	0.2997	142	0.2326	2720	X-RAY DIFFRACTION	100
2.78-2.86	0.291	142	0.2226	2707	X-RAY DIFFRACTION	100
2.86-2.96	0.2746	129	0.212	2686	X-RAY DIFFRACTION	100
2.96-3.06	0.2189	133	0.2084	2716	X-RAY DIFFRACTION	100
3.06-3.18	0.2442	150	0.196	2727	X-RAY DIFFRACTION	100
3.18-3.33	0.2038	149	0.1753	2681	X-RAY DIFFRACTION	100
3.33-3.5	0.2027	131	0.1691	2717	X-RAY DIFFRACTION	100
3.5-3.72	0.2141	134	0.1577	2714	X-RAY DIFFRACTION	99
3.72-4.01	0.2141	171	0.1578	2668	X-RAY DIFFRACTION	99
4.01-4.41	0.1625	149	0.1387	2699	X-RAY DIFFRACTION	99
4.42-5.05	0.1513	152	0.1294	2686	X-RAY DIFFRACTION	100
5.05-6.36	0.1801	159	0.1614	2730	X-RAY DIFFRACTION	100
6.36-41.31	0.1899	168	0.182	2728	X-RAY DIFFRACTION	99

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	1.2234	-0.0683	-0.7045	0.6325	-0.5299	1.9245	-0.1289	-0.136	0.1249	0.0711	-0.0585	-0.1119	0.0089	0.3137	0.1318	0.1359	-0.016	-0.0176	0.1284	0.0472	0.1378	28.4356	38.3067	20.274
2	1.5074	0.67	-0.2953	1.365	-0.0746	0.8919	0.1479	-0.1235	0.3295	0.2673	-0.1013	0.1494	-0.0874	-0.193	-0.0502	0.1079	0.0099	0.0282	0.1761	0.0419	0.1418	22.0529	44.9776	20.1595
3	1.1185	0.2716	0.8402	0.7906	-0.0831	1.5023	0.1294	-0.1177	0.1887	0.1166	-0.0485	0.0585	0.108	-0.1906	-0.1136	0.1039	0.0303	0.0151	0.1271	0.1034	0.2037	19.1507	40.003	17.7911
4	1.5354	-0.297	0.4056	0.3735	-0.5965	1.6234	0.1759	0.0121	-0.2451	0.3915	-0.0987	-0.2699	-0.0499	0.1113	-0.1081	0.288	-0.0084	-0.0434	0.4751	-0.0286	0.1591	23.203	19.2406	41.8959
5	1.1655	0.5261	-0.18	1.8875	-0.0481	2.035	0.0169	0.2267	-0.2683	-0.1349	0.0845	-0.5484	-0.0572	0.5671	-0.0219	0.1639	0.0072	0.0314	0.4502	-0.0231	0.2515	22.5902	13.4739	35.6885
6	1.7225	-1.5111	0.296	2.8186	0.9915	1.1235	0.0419	0.0615	-0.2708	0.0626	-0.0525	-0.6792	0.0304	0.3541	0.0255	0.269	0.01	-0.0532	0.5957	0.0069	0.5021	30.6191	13.7112	38.7607
7	1.5021	-0.164	-0.2008	3.4937	0.2088	0.6199	-0.0239	-0.0152	0.0661	-0.2137	-0.0494	0.3069	0.1275	-0.182	0.0313	0.1367	-0.0327	0.018	0.2279	0.0235	0.0576	3.2082	30.8314	11.5814
8	0.2952	0.0335	-0.1972	1.2705	-0.9715	0.8654	0.0072	-0.0574	0.0216	-0.0185	-0.0848	-0.1422	0.1351	0.128	0.0708	0.1553	0.0105	0.0098	0.2221	0.0223	0.1193	10.5967	21.5551	20.0589
9	0.5802	0.2233	0.4342	1.2151	0.4456	1.295	-0.0984	0.0902	-0.1937	0.0375	-0.006	-0.0795	-0.0713	0.1776	0.0634	0.2137	0.0082	0.0348	0.327	0.0046	0.1129	6.4106	11.735	36.9614
10	0.5669	0.4818	0.6848	1.3594	0.3689	4.3815	0.1445	-0.1886	-0.282	0.2975	-0.0535	-0.2334	0.3322	-0.0941	-0.0065	0.2667	0.0005	-0.0116	0.39	0.093	0.1154	9.1253	5.748	46.2829
11	3.1074	0.0026	1.0539	0.7796	1.124	1.9739	-0.2009	0.4025	-0.1178	-0.3483	0.3137	0.1748	0.3293	0.1026	-0.0418	0.2621	0.0037	-0.1234	0.1383	-0.0181	0.2393	52.166	9.0567	6.6292
12	0.9409	0.1144	0.1566	0.4701	0.2654	0.779	0.2347	0.037	-0.1836	0.0995	0.1005	-0.1906	0.3913	-0.0042	-0.1945	0.2259	-0.0249	-0.1456	0.1582	-0.0164	0.2937	58.2256	13.0399	16.4263
13	4.0406	0.322	-0.5244	1.5528	-0.1682	1.3385	0.205	-0.0537	-0.3591	0.2801	0.1361	-0.1629	0.5015	0.0008	-0.2313	0.3661	-0.0385	-0.1715	0.1908	0.0149	0.3238	56.2182	6.3801	18.4554
14	0.5253	0.2086	0.7681	1.826	0.0292	1.1659	0.1036	-0.2135	-0.3943	0.2222	0.0842	0.097	0.2734	-0.1566	-0.0223	0.3079	-0.0584	-0.155	0.1479	0.0505	0.3565	49.4138	6.0414	14.0609
15	0.2995	0.0135	-0.1368	0.4285	0.2727	0.9024	-0.0016	-0.0843	-0.1027	0.0927	-0.0443	-0.0152	0.1322	-0.0768	-0.2775	0.1254	-0.0768	-0.1824	0.0673	0.0005	0.2333	53.6028	15.6662	13.0464
16	3.3296	1.9726	-0.0761	3.2954	0.5556	1.4069	-0.0847	0.3477	0.1595	-0.5898	0.2212	0.2776	-0.2764	-0.093	-0.1854	0.2738	0.0032	-0.0088	0.1396	-0.0004	0.1569	36.3563	19.3514	-15.9316
17	1.4521	-0.2913	0.2314	1.9847	0.0965	0.8765	0.1242	0.1561	0.0928	-0.2021	-0.0818	-0.4122	0.1569	0.0007	-0.0075	0.1654	-0.0035	0.0092	0.1082	-0.0374	0.2322	41.2575	18.7084	-7.469
18	2.4733	-0.0417	0.2099	1.8652	0.4092	1.351	0.0927	0.6984	0.2022	-0.7513	-0.0802	-0.4536	-0.1404	-0.0258	0.0299	0.3997	0.0305	0.1367	0.2556	0.0424	0.2534	41.5419	24.9336	-18.1903
19	2.368	-0.3595	-0.8483	4.5634	-1.1759	2.2038	0.2251	0.5402	-0.0595	-0.7105	-0.1944	-0.2846	-0.0446	0.0356	-0.0935	0.3108	0.0452	0.0854	0.2197	-0.0656	0.2705	43.0734	14.2722	-17.3098
20	1.4218	-0.7077	1.1205	1.6241	-0.8622	2.4848	-0.0573	-0.1606	0.1974	0.3154	0.0125	-0.1252	-0.202	-0.022	0.078	0.1476	-0.032	-0.0232	0.1086	0.005	0.1974	47.8682	35.8778	21.1555
21	2.9168	-0.2994	0.1602	1.8382	-0.5364	0.426	0.0394	0.3734	-0.0417	-0.254	-0.0722	0.1621	0.0241	0.0591	-0.0159	0.0656	0.0062	-0.0898	0.103	-0.0149	0.2106	53.2612	29.1353	11.3054
22	1.0684	-0.6651	1.0132	0.5291	-0.3898	1.4121	0.0484	-0.0111	0.19	0.0325	0.0134	-0.1643	-0.0209	0.1145	0.028	0.1329	-0.0291	-0.0494	0.0907	0.032	0.2012	51.4745	35.2372	13.6668
23	0.7168	0.4029	0.296	1.4974	0.5778	1.1657	0.0418	0.1708	-0.0317	-0.2733	0.0131	0.236	0.0404	-0.0243	-0.0447	0.174	0.0153	-0.0758	0.1155	0.0308	0.2354	29.7645	27.1334	-9.7661
24	0.904	0.5021	0.2607	1.2984	0.0953	0.5156	0.0834	0.3876	-0.2326	-0.5441	0.0069	0.4739	0.1473	-0.0252	-0.0822	0.3052	0.0287	-0.2601	0.2228	0.0113	0.3898	22.5189	26.3535	-15.8338

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 33 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 34 through 82 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 82A through 109 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 110 through 135 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 136 through 193 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 194 through 215 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 1 through 39 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 40 through 139 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 140 through 172 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 173 through 214 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 1 through 17 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 18 through 59 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 60 through 75 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 76 through 87 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 88 through 119 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 120 through 145 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 146 through 175 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 176 through 193 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 194 through 216 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 1 through 32 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 33 through 48 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 49 through 113 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 114 through 174 )
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 175 through 214 )

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