PDB-9mzv: anti-IL6 designed Fab

ID or keywords:

Entry

Database: PDB / ID: 9mzv

Title

anti-IL6 designed Fab

Components

(anti-IL6 designed Fab ...) x 2

Keywords

IMMUNE SYSTEM / design / pharmacology / antibody / machine learning

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Kiefer, J.R. / Alberstein, R.G. / Frey, N.C. / Seeger, F. / Dou, Y. / Huo, C. / Watkins, A.M. / Leaver-Fay, A. / Hofmann, J.L. / Gligorijevic, V. / Bonneau, R.

Funding support

1items

Citation

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

History

Deposition	Jan 23, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 9, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9mzv.cif.gz	363.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9mzv.ent.gz	293.4 KB	Display	PDB format
PDBx/mmJSON format	9mzv.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/mz/9mzv ftp://data.pdbj.org/pub/pdb/validation_reports/mz/9mzv	HTTPS FTP

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Related structure data

Related structure data	9muyC 9muzC 9mvjC 9mzcC 9n2vC 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: anti-IL6 designed Fab heavy chain

L: anti-IL6 designed Fab light chain

A: anti-IL6 designed Fab heavy chain

B: anti-IL6 designed Fab light chain

hetero molecules

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

1

H: anti-IL6 designed Fab heavy chain

L: anti-IL6 designed Fab light chain

hetero molecules

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

2

A: anti-IL6 designed Fab heavy chain

B: anti-IL6 designed Fab light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.590, 60.210, 94.450
Angle α, β, γ (deg.)	90.00, 96.41, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Antibody , 2 types, 4 molecules HALB

#1: Antibody	anti-IL6 designed Fab heavy chain Mass: 23987.893 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	anti-IL6 designed Fab light chain Mass: 23069.482 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, 859 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 839 / 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: 2.45 Å³/Da / Density % sol: 49.79 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Calcium chloride, 0.1M Tris-HCl pH 8.5 , 20% w/v PEG 4000

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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: 1.9→48.34 Å / Num. obs: 71337 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.134 / R_pim(I) all: 0.055 / R_rim(I) all: 0.145 / Χ²: 0.99 / Net I/σ(I): 12.4 / Num. measured all: 495512
Reflection shell	Resolution: 1.9→1.94 Å / % possible obs: 99.1 % / Redundancy: 6.9 % / R_merge(I) obs: 1.035 / Num. measured all: 31840 / Num. unique obs: 4607 / CC_1/2: 0.676 / R_pim(I) all: 0.422 / R_rim(I) all: 1.12 / Χ²: 0.93 / Net I/σ(I) obs: 2.2

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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: 1.9→48.34 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2142	3484	4.88 %
R_work	0.1768	-	-
obs	0.1787	71330	99.14 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→48.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6545	0	35	839	7419

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6812
X-RAY DIFFRACTION	f_angle_d	0.591	9288
X-RAY DIFFRACTION	f_dihedral_angle_d	11.425	2415
X-RAY DIFFRACTION	f_chiral_restr	0.045	1054
X-RAY DIFFRACTION	f_plane_restr	0.005	1201

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 (%)
1.9-1.93	0.2843	156	0.2298	2706	X-RAY DIFFRACTION	99
1.93-1.95	0.2708	154	0.2175	2647	X-RAY DIFFRACTION	99
1.95-1.98	0.2498	112	0.2038	2735	X-RAY DIFFRACTION	99
1.98-2.01	0.2167	130	0.2009	2704	X-RAY DIFFRACTION	99
2.02-2.05	0.246	142	0.2014	2661	X-RAY DIFFRACTION	99
2.05-2.08	0.2866	148	0.2082	2679	X-RAY DIFFRACTION	98
2.08-2.12	0.2603	145	0.2055	2600	X-RAY DIFFRACTION	96
2.12-2.16	0.2341	135	0.193	2713	X-RAY DIFFRACTION	99
2.16-2.21	0.2545	143	0.1824	2725	X-RAY DIFFRACTION	100
2.21-2.25	0.2334	132	0.1853	2727	X-RAY DIFFRACTION	100
2.25-2.31	0.271	149	0.1882	2715	X-RAY DIFFRACTION	100
2.31-2.36	0.2282	132	0.1878	2716	X-RAY DIFFRACTION	100
2.36-2.43	0.2371	133	0.1898	2728	X-RAY DIFFRACTION	100
2.43-2.5	0.2672	139	0.2012	2740	X-RAY DIFFRACTION	100
2.5-2.58	0.2308	131	0.1979	2707	X-RAY DIFFRACTION	100
2.58-2.67	0.222	146	0.1916	2746	X-RAY DIFFRACTION	100
2.67-2.78	0.2276	144	0.183	2693	X-RAY DIFFRACTION	100
2.78-2.91	0.2177	132	0.1864	2746	X-RAY DIFFRACTION	99
2.91-3.06	0.238	145	0.1832	2704	X-RAY DIFFRACTION	99
3.06-3.25	0.2226	163	0.1835	2701	X-RAY DIFFRACTION	99
3.25-3.5	0.206	130	0.1703	2751	X-RAY DIFFRACTION	99
3.5-3.85	0.1659	114	0.1511	2670	X-RAY DIFFRACTION	96
3.85-4.41	0.148	140	0.1364	2698	X-RAY DIFFRACTION	98
4.41-5.56	0.1577	147	0.134	2789	X-RAY DIFFRACTION	100
5.56-48.34	0.2168	142	0.1935	2845	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	0.8421	0.1035	-0.0549	2.6404	0.5647	1.1128	0.0073	0.0393	0.0112	-0.0364	-0.0534	0.1545	0.0011	-0.1045	0.0214	0.1382	-0.0004	-0.0019	0.1325	-0.0036	0.1715	-1.7856	15.9597	-42.1753
2	0.5911	0.5787	-0.2614	1.4829	-0.6953	1.1189	0.0306	-0.144	0.0064	0.1911	0.0614	0.113	0.095	-0.112	0.015	0.1993	0.0094	0.024	0.1915	0.0057	0.2095	-6.8404	0.9811	-22.2848
3	1.0738	0.6324	-0.1769	1.8819	1.2679	5.8279	-0.035	-0.1474	0.0992	0.0869	0.0294	0.2383	-0.0102	-0.3561	0.0468	0.1604	0.0348	-0.0018	0.2154	0.0262	0.2058	-10.6962	-1.1541	-15.7668
4	2.0882	-0.3644	-3.3591	1.7179	-0.0566	6.0741	0.1363	-0.2791	0.0217	0.1288	-0.1329	-0.1056	-0.0351	0.3667	-0.0841	0.1234	-0.0263	-0.0149	0.2323	-0.0158	0.2079	19.5046	15.9189	-23.5316
5	1.2957	0.3945	0.0127	2.1365	-0.6349	1.9944	0.0667	-0.1066	0.1982	0.1868	-0.0264	0.058	-0.1371	0.085	-0.0444	0.1217	-0.006	0.0184	0.1281	-0.0235	0.1739	12.8763	21.9286	-27.9194
6	1.3921	2.2879	-3.3944	3.7277	-5.5846	8.3862	0.1388	-0.2526	-0.1066	0.3059	-0.2281	0.0049	-0.353	0.3293	0.0315	0.247	-0.0263	-0.0029	0.2645	-0.0018	0.1995	12.2011	9.1119	-9.5045
7	5.1349	4.0785	3.529	9.0764	4.8904	7.8188	-0.0537	-0.279	-0.0455	-0.3549	-0.1888	0.7538	0.3154	-0.7531	0.1591	0.2641	-0.0492	-0.0019	0.2906	0.0711	0.2568	-8.8082	-13	-10.4695
8	2.3585	3.3524	-0.1831	7.3462	0.803	0.6192	-0.0391	-0.2371	-0.1279	0.019	-0.1167	-0.2613	-0.0268	0.0025	0.1342	0.2347	0.0296	-0.0045	0.2516	0.0376	0.1429	4.9367	-7.0414	-9.1015
9	0.924	1.5759	-0.2948	6.5862	-1.1744	1.4499	0.0538	-0.072	-0.035	-0.0853	-0.1438	0.1071	0.0804	0.1619	0.0888	0.1801	0.0251	0.0135	0.2714	-0.0073	0.1763	5.3337	-3.1423	-12.2071
10	1.9818	2.4875	0.0238	6.278	0.6655	2.2268	0.1766	-0.177	-0.2596	0.229	-0.1445	-0.1253	0.3964	0.0206	-0.0468	0.1944	0.0492	0.0156	0.19	0.0513	0.175	1.1109	-15.6238	-6.4568
11	1.127	0.9839	0.0962	4.5091	0.1745	1.5839	-0.0089	-0.057	-0.0076	0.1708	0.0175	-0.3489	-0.024	0.2163	-0.0228	0.1164	0.0109	-0.0107	0.1799	-0.0124	0.1863	-27.9271	7.4186	-36.7544
12	0.9236	0.8446	-0.4125	2.2114	-0.3176	1.44	-0.0352	0.0367	-0.0652	-0.0499	0.0584	-0.1439	0.1016	0.1322	-0.0232	0.1058	0.0161	-0.007	0.1255	-0.0173	0.1685	-31.4236	6.3669	-42.8528
13	0.8512	0.6218	0.3557	1.6939	1.0519	2.7063	0.1539	-0.2901	0.0159	0.2953	0.0042	-0.1514	-0.139	0.1473	-0.0788	0.2152	-0.0045	-0.0133	0.2655	-0.0311	0.1966	-29.5797	22.7037	-18.6698
14	1.8606	0.555	-0.0745	2.9006	-0.4298	2.5736	-0.0513	-0.2443	-0.0499	0.1334	0.07	-0.2751	-0.1134	-0.1528	0.0084	0.2021	-0.0452	-0.0174	0.263	-0.0259	0.2081	-30.0981	22.2834	-14.4606
15	3.0514	0.6024	1.8347	2.1149	0.7128	6.7324	0.1942	-0.5316	0.0505	0.3187	-0.0285	-0.4309	-0.3925	0.66	-0.237	0.3672	-0.0827	-0.0715	0.4594	-0.0589	0.4248	-20.8601	24.1952	-9.2025
16	1.7878	-0.1511	1.473	2.226	0.4128	3.8813	0.0828	-0.4416	0.0883	0.2399	-0.1639	0.1328	0.2172	-0.4596	0.0851	0.1181	-0.0459	0.0183	0.2625	-0.0251	0.1836	-54.8476	8.131	-26.4456
17	2.4703	0.6759	-0.021	2.2934	0.9603	2.1839	0.0707	-0.1529	-0.2274	0.2925	-0.0671	0.0333	0.2424	-0.1329	0.0118	0.1491	-0.0025	-0.0072	0.117	0.02	0.1393	-48.7998	1.521	-30.4317
18	0.4757	0.8936	1.6716	1.6605	3.0943	5.9362	0.1747	-0.5616	0.1521	0.1753	-0.1901	-0.0203	-0.338	-0.5651	0.0377	0.2538	-0.0523	0.039	0.4347	-0.0424	0.1952	-50.9278	13.884	-12.0601
19	0.73	0.696	-0.2086	4.1351	1.1886	3.1112	0.0293	-0.2306	0.178	-0.1421	-0.0265	-0.006	-0.5007	-0.0162	-0.0142	0.3168	0.0123	-0.0097	0.3918	-0.0649	0.2101	-39.2238	33.3125	-10.2915
20	0.9951	2.1677	0.69	6.6399	2.5026	2.379	-0.0763	-0.0553	0.0941	-0.3051	0.0541	-0.0235	-0.4091	-0.0613	0.016	0.2926	-0.0057	-0.0164	0.3899	-0.0212	0.2275	-39.5517	31.7367	-10.5025
21	4.8914	4.0114	0.9735	3.5621	1.4218	3.8034	0.6576	-0.4747	0.162	0.988	-0.6161	-0.0376	-0.2491	-0.0857	0.0662	0.4108	0.0169	0.0011	0.4382	-0.0534	0.3641	-42.3089	35.3139	-1.5053

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 100B)
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 100C through 134 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 135 through 215 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 1 through 25 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 26 through 101 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 102 through 113 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 114 through 128 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 129 through 150 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 151 through 174 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 175 through 213 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 1 through 43 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 44 through 100B)
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 100C through 145 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 146 through 188 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 189 through 216 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 1 through 18 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 19 through 101 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 102 through 113 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 114 through 163 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 164 through 197 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 198 through 214 )

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