PDB-9n2v: Designed anti-OSM Fab

ID or keywords:

Entry

Database: PDB / ID: 9n2v

Title

Designed anti-OSM Fab

Components

(designed anti-OSM Fab ...) x 2

Keywords

IMMUNE SYSTEM / Fab / antibody / machine learning / AI / design

Function / homology

PHOSPHATE ION

Function and homology information

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.97 Å

Authors

Kiefer, J.R. / Alberstein, R.G. / Watkins, A.M. / Seeger, F. / Frey, N.C. / Bonneau, R. / Regev, A. / Hofmann, J.L. / Gligorijevic, V.

Funding support

1items

Citation

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

History

Deposition	Jan 29, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 4, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9n2v.cif.gz	367.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9n2v.ent.gz	300.1 KB	Display	PDB format
PDBx/mmJSON format	9n2v.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/n2/9n2v ftp://data.pdbj.org/pub/pdb/validation_reports/n2/9n2v	HTTPS FTP

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Related structure data

Related structure data	9n7mC 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.)
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)

Deposited unit

H: designed anti-OSM Fab heavy chain

L: designed anti-OSM Fab light chain

A: designed anti-OSM Fab heavy chain

B: designed anti-OSM Fab light chain

hetero molecules

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

1

H: designed anti-OSM Fab heavy chain

L: designed anti-OSM Fab light chain

hetero molecules

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

2

A: designed anti-OSM Fab heavy chain

B: designed anti-OSM Fab light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	117.890, 117.890, 99.170
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 anti-OSM Fab heavy chain Mass: 24371.301 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 anti-OSM 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, 882 molecules

#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 853 / 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: 3.63 Å³/Da / Density % sol: 66.09 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M sodium chloride, 0.1 M imidazole, pH 8.0, 0.4 M ammonium phosphate, 1.6 M potassium phosphate dibasic

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Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03321 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 4, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03321 Å / Relative weight: 1
Reflection	Resolution: 1.97→46.55 Å / Num. obs: 95394 / % possible obs: 99.5 % / Redundancy: 13.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.154 / R_pim(I) all: 0.043 / R_rim(I) all: 0.16 / Χ²: 1 / Net I/σ(I): 16.1 / Num. measured all: 1308844
Reflection shell	Resolution: 1.97→2 Å / % possible obs: 100 % / Redundancy: 13.4 % / R_merge(I) obs: 1.62 / Num. measured all: 63068 / Num. unique obs: 4704 / CC_1/2: 0.745 / R_pim(I) all: 0.457 / R_rim(I) all: 1.684 / Χ²: 0.86 / Net I/σ(I) obs: 2.1

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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: 1.97→46.55 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2022	4880	5.12 %
R_work	0.1741	-	-
obs	0.1755	95351	99.49 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.97→46.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6525	0	116	853	7494

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6921
X-RAY DIFFRACTION	f_angle_d	0.589	9400
X-RAY DIFFRACTION	f_dihedral_angle_d	11.704	2467
X-RAY DIFFRACTION	f_chiral_restr	0.046	1050
X-RAY DIFFRACTION	f_plane_restr	0.004	1212

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 (%)
1.97-1.99	0.3106	162	0.2753	2995	X-RAY DIFFRACTION	100
1.99-2.02	0.2973	166	0.2534	2990	X-RAY DIFFRACTION	100
2.02-2.04	0.2884	141	0.2396	3105	X-RAY DIFFRACTION	100
2.04-2.07	0.2807	178	0.2321	2958	X-RAY DIFFRACTION	100
2.07-2.09	0.3626	141	0.3069	2972	X-RAY DIFFRACTION	98
2.09-2.12	0.2687	154	0.2246	3000	X-RAY DIFFRACTION	99
2.12-2.15	0.2417	190	0.2132	3003	X-RAY DIFFRACTION	100
2.15-2.18	0.2479	191	0.206	2991	X-RAY DIFFRACTION	100
2.18-2.22	0.2685	155	0.2091	3033	X-RAY DIFFRACTION	100
2.22-2.25	0.2773	196	0.2301	2907	X-RAY DIFFRACTION	97
2.25-2.29	0.4207	135	0.3615	2759	X-RAY DIFFRACTION	92
2.29-2.34	0.2347	159	0.2025	3041	X-RAY DIFFRACTION	100
2.34-2.38	0.2349	191	0.1926	2977	X-RAY DIFFRACTION	100
2.38-2.43	0.2089	159	0.1912	3033	X-RAY DIFFRACTION	100
2.43-2.48	0.2283	181	0.1803	3031	X-RAY DIFFRACTION	100
2.48-2.54	0.2154	153	0.1763	3014	X-RAY DIFFRACTION	100
2.54-2.6	0.2061	150	0.1756	3039	X-RAY DIFFRACTION	100
2.6-2.67	0.2004	183	0.1785	2983	X-RAY DIFFRACTION	100
2.67-2.75	0.1889	161	0.1799	3062	X-RAY DIFFRACTION	100
2.75-2.84	0.212	159	0.1777	3005	X-RAY DIFFRACTION	100
2.84-2.94	0.2569	132	0.1822	3085	X-RAY DIFFRACTION	100
2.94-3.06	0.2081	173	0.1759	3000	X-RAY DIFFRACTION	100
3.06-3.2	0.2166	190	0.1717	3033	X-RAY DIFFRACTION	100
3.2-3.37	0.199	174	0.1667	3003	X-RAY DIFFRACTION	100
3.37-3.58	0.1823	164	0.1527	3056	X-RAY DIFFRACTION	100
3.58-3.85	0.1892	125	0.1436	3058	X-RAY DIFFRACTION	100
3.85-4.24	0.1441	131	0.1321	3063	X-RAY DIFFRACTION	100
4.24-4.86	0.1138	158	0.1163	3083	X-RAY DIFFRACTION	100
4.86-6.12	0.1498	158	0.1408	3070	X-RAY DIFFRACTION	100
6.12-46.55	0.1774	170	0.1839	3122	X-RAY DIFFRACTION	100

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	2.7114	0.4991	-0.4028	1.2356	-2.0319	3.4275	0.0932	-0.4112	0.0874	0.6041	0.0905	-0.2691	0.5473	0.3258	-0.1518	0.2646	-0.0303	-0.0569	0.2358	0.046	0.2179	27.4471	37.373	26.8809
2	2.4213	-0.9443	-2.8832	1.6736	-0.1987	4.7084	0.0994	-0.1543	0.0307	0.1354	-0.0303	-0.2605	0.0021	0.3916	-0.0785	0.2069	-0.0391	-0.0454	0.2759	0.0468	0.2822	30.45	39.9985	13.8257
3	2.2469	0.5257	1.1396	5.2291	-0.895	2.0791	0.11	-0.1923	0.0787	0.2968	-0.1866	0.0952	-0.0762	-0.0696	0.0639	0.1596	0.0024	0.0053	0.2221	-0.0067	0.148	19.6304	44.0035	18.0623
4	5.1592	-0.4313	-3.2452	3.2799	0.7504	4.8745	0.183	-0.2655	0.4363	0.3693	-0.0834	-0.222	-0.1723	0.0348	-0.0763	0.2434	-0.0093	-0.0441	0.2488	-0.011	0.2238	26.7009	46.8183	21.1517
5	0.7283	0.0922	0.5458	2.0119	-0.8069	3.3919	0.0922	-0.1891	0.1472	0.2231	-0.0579	0.0464	0.0019	-0.1296	-0.034	0.1946	-0.0327	0.0181	0.3243	0.0356	0.2555	19.8622	39.9462	17.998
6	0.4929	1.0932	-0.5047	4.0152	-1.9877	1.1161	0.1381	-0.1662	-0.2529	0.0488	-0.1624	-0.4357	-0.217	0.0652	0.0833	0.4282	-0.0943	-0.1178	0.4935	0.0122	0.2519	23.2723	20.3134	42.7151
7	2.6308	0.7064	1.3919	3.9467	-0.1614	3.9979	0.0243	0.1429	-0.3202	0.0752	-0.0086	-0.766	0.0068	0.786	-0.0252	0.2485	-0.0485	0.0172	0.5379	0.0093	0.3923	24.8166	14.5403	36.7841
8	1.4493	-2.8775	-0.4306	7.7091	-0.0586	1.793	-0.0174	0.0292	-0.0278	0.2629	-0.0612	0.416	0.2751	-0.1392	0.0985	0.2139	-0.067	0.0217	0.3276	-0.0037	0.2492	0.9305	27.3274	14.9025
9	2.6583	-0.5609	0.3422	4.3836	-1.3682	1.9737	-0.0083	0.2881	0.3148	-0.1587	-0.0445	0.1776	0.0961	-0.116	0.0576	0.2119	-0.0442	0.0045	0.2845	0.041	0.1914	4.463	34.006	8.8165
10	4.9143	-0.1431	2.9379	5.0093	-3.4835	4.0642	0.1136	0.1107	-0.4771	-0.158	-0.2627	-0.3273	0.4097	0.9129	0.1597	0.22	0.046	0.0376	0.3102	0.0634	0.2513	16.164	26.3971	14.2096
11	1.6308	0.4909	-0.0975	4.3007	-1.4344	2.3474	-0.0543	0.1922	0.0627	-0.3096	-0.0078	-0.0444	0.2551	-0.03	0.058	0.1781	-0.0258	0.0221	0.2857	0.0199	0.2083	8.2015	30.0208	8.5221
12	-0.0042	0.201	-0.2023	4.0079	-4.6463	5.3394	-0.0369	-0.0197	0.0371	0.0057	-0.0695	-0.0745	0.2719	0.2102	0.1003	0.2701	-0.0341	0.0303	0.3299	0.0177	0.2401	3.8933	12.563	21.402
13	3.583	3.4967	3.1982	6.2737	4.5743	3.6655	0.0281	-0.1687	-0.5408	0.3757	-0.0091	-1.1924	0.0007	0.7073	-0.1554	0.396	-0.0456	-0.166	0.6112	0.1477	0.4193	19.5478	8.7568	47.7082
14	1.0043	-0.3337	1.5178	1.7282	0.3575	9.2257	-0.1978	-0.018	-0.0877	0.1105	0.1628	-0.0857	-0.3296	-0.1333	0.0706	0.3553	-0.0264	0.0201	0.3534	0.0386	0.2288	7.3524	10.3207	38.5146
15	1.2876	-0.1713	0.0707	2.0468	0.0938	3.8575	0.1045	-0.1641	0.0154	0.1107	0.1079	-0.1638	-0.5254	0.6761	-0.1997	0.3017	-0.0523	-0.0081	0.3507	0.0157	0.2614	8.1748	13.2413	35.5625
16	2.1533	0.657	0.181	3.139	-0.4391	4.2836	-0.0186	-0.6147	-0.2586	0.3638	-0.0781	-0.2992	0.087	0.0369	0.0889	0.2965	0.0423	-0.0001	0.4938	0.0633	0.2179	8.4795	6.4874	47.3417
17	8.1709	3.3403	3.1814	2.9271	2.6988	2.4994	-0.1893	0.5202	-0.3461	-0.4836	0.4589	-0.0136	0.4143	-0.0693	-0.2151	0.3211	-0.0182	-0.1047	0.1971	-0.0053	0.2561	53.596	8.9662	5.8441
18	1.8413	0.1936	0.2416	2.1326	0.0534	2.0049	0.1054	-0.0177	-0.2379	-0.0452	0.115	0.0276	0.2885	-0.0313	-0.2097	0.2472	-0.0548	-0.0891	0.1681	-0.0031	0.2659	59.7371	13.1972	15.5066
19	2.4862	0.2853	-2.962	2.2408	-0.3587	3.7322	-0.0513	-0.0198	-0.4696	0.0907	0.1687	0.089	0.6547	-0.165	-0.0979	0.3382	-0.0501	-0.117	0.2709	0.0093	0.3015	58.2757	6.3093	17.6045
20	1.8487	0.2464	2.0918	0.4134	1.1221	2.3713	0.1514	0.008	-0.2528	0.0386	-0.0207	-0.0242	0.1872	-0.0937	-0.1511	0.2585	-0.0539	-0.0528	0.2111	0.0051	0.2645	51.6999	13.2534	9.0058
21	2.2525	-0.7332	1.1419	4.2708	-0.0999	1.5323	0.2601	0.5641	0.0533	-0.5863	-0.3511	-0.525	-0.0344	0.2418	0.1109	0.2993	0.0816	0.0687	0.3065	0.0041	0.3202	42.2428	18.1387	-12.9112
22	3.5024	-1.338	1.8992	0.5418	-0.9387	6.6046	-0.0519	-0.2984	0.139	0.0069	0.1813	0.1361	0.0622	-0.4533	-0.1606	0.1606	-0.0051	-0.0062	0.2382	0.0209	0.3232	44.9336	36.2746	16.619
23	3.1025	-1.5178	1.2574	1.8756	-1.8283	5.2759	-0.1538	-0.357	0.3009	0.2851	0.1273	0.04	-0.2545	-0.1598	0.0415	0.2047	-0.02	-0.047	0.2385	-0.004	0.3224	52.8036	33.6667	21.7037
24	2.7664	-1.2829	1.6988	2.3304	-1.3129	3.6105	0.0454	0.025	0.1822	0.0153	0.0243	-0.0238	-0.0759	0.0046	-0.0585	0.1748	-0.0242	-0.0231	0.2104	0.0037	0.2713	54.8779	32.9152	15.3273
25	5.0243	-3.7901	5.0241	2.8703	-3.7949	4.9874	-0.1783	-0.155	0.2008	0.118	-0.0439	-0.4064	-0.0576	-0.1009	0.2377	0.2094	-0.0282	-0.0441	0.2195	0.0397	0.3184	40.092	40.0766	0.8787
26	2.4214	1.2483	0.9524	6.407	0.9131	1.9044	0.0856	0.2222	-0.088	-0.3664	-0.0652	0.2312	0.1906	-0.0729	-0.0104	0.2227	0.0353	-0.0368	0.197	-0.0031	0.2192	27.6813	25.0533	-11.662
27	4.5597	6.4569	4.7345	9.6464	6.178	5.8374	0.1205	0.2316	-0.6649	0.173	0.0812	-1.0717	0.2673	0.2972	-0.1141	0.2299	0.0283	-0.03	0.2546	0.0202	0.3801	42.9897	34.4135	-3.4412
28	0.8363	-0.713	0.1513	0.9294	-0.6387	0.8001	0.1735	0.2676	-0.2772	-0.7292	-0.1256	0.7296	0.2339	-0.058	0.0042	0.3682	0.0407	-0.1688	0.2439	-0.061	0.4139	23.0386	26.2929	-15.713

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 18 through 33 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 34 through 59 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 60 through 82 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 82A through 109 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 110 through 134 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 135 through 214 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 1 through 17 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 18 through 38 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 39 through 48 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 49 through 101 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 102 through 113 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 114 through 128 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 129 through 150 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 151 through 174 )
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 175 through 213 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 1 through 17 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 18 through 59 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 60 through 75 )
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 76 through 134 )
21	X-RAY DIFFRACTION	21	chain 'A' and (resid 135 through 214 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 1 through 17 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 18 through 38 )
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 39 through 101 )
25	X-RAY DIFFRACTION	25	chain 'B' and (resid 102 through 113 )
26	X-RAY DIFFRACTION	26	chain 'B' and (resid 114 through 163 )
27	X-RAY DIFFRACTION	27	chain 'B' and (resid 164 through 174 )
28	X-RAY DIFFRACTION	28	chain 'B' and (resid 175 through 213 )

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The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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Antibody , 2 types, 4 molecules HALB

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Non-polymers , 4 types, 882 molecules

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-Antibody , 2 types, 4 molecules HALB

-Non-polymers , 4 types, 882 molecules

-Details

-Experimental details

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+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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Validation report

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Components

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Antibody , 2 types, 4 molecules HALB

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Non-polymers , 4 types, 882 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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Data collection

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Processing

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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