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- PDB-9muz: anti-IL6 designed Fab -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9muz
Titleanti-IL6 designed Fab
Components(anti-IL6 Fab ...) x 2
KeywordsIMMUNE SYSTEM / antibody / design / machine learning / fab / IL6
Function / homologyL(+)-TARTARIC ACID
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsKiefer, J.R. / Frey, N.C. / Alberstein, R.G. / Seeger, F. / Watkins, A.M. / Gligorijevic, V. / Dou, Y. / Tang, Y. / Regev, A. / Bonneau, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Lab-in-the-loop therapeutic antibody design with deep learning
Authors: Frey, N.C. / Seeger, F. / Kiefer, J.R. / Alberstein, R.G. / Watkins, A.M. / Bonneau, R. / Regev, A. / Hotzel, I.
History
DepositionJan 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: anti-IL6 Fab heavy chain
L: anti-IL6 Fab light chain
A: anti-IL6 Fab heavy chain
B: anti-IL6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,03317
Polymers94,2314
Non-polymers80313
Water16,844935
1
H: anti-IL6 Fab heavy chain
L: anti-IL6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,52010
Polymers47,1152
Non-polymers4048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-21 kcal/mol
Surface area18900 Å2
MethodPISA
2
A: anti-IL6 Fab heavy chain
B: anti-IL6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5147
Polymers47,1152
Non-polymers3985
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-20 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.017, 147.329, 61.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Antibody , 2 types, 4 molecules HALB

#1: Antibody anti-IL6 Fab heavy chain


Mass: 24045.889 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 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 , 5 types, 948 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 935 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2 M Sodium Potassium phosphate, 20 % v/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.71→147.33 Å / Num. obs: 91871 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.043 / Rrim(I) all: 0.116 / Χ2: 1.04 / Net I/σ(I): 11.3 / Num. measured all: 644863
Reflection shellResolution: 1.71→1.74 Å / % possible obs: 100 % / Redundancy: 6 % / Rmerge(I) obs: 0.861 / Num. measured all: 26991 / Num. unique obs: 4507 / CC1/2: 0.689 / Rpim(I) all: 0.378 / Rrim(I) all: 0.942 / Χ2: 0.77 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→73.66 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 19.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1961 8797 5.01 %
Rwork0.166 --
obs0.1675 91776 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→73.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6551 0 49 935 7535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046903
X-RAY DIFFRACTIONf_angle_d0.6449410
X-RAY DIFFRACTIONf_dihedral_angle_d12.182465
X-RAY DIFFRACTIONf_chiral_restr0.0471057
X-RAY DIFFRACTIONf_plane_restr0.0061225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.730.31433130.28185565X-RAY DIFFRACTION100
1.73-1.750.29993200.26795540X-RAY DIFFRACTION100
1.75-1.770.25512760.25875570X-RAY DIFFRACTION100
1.77-1.80.2883050.23575594X-RAY DIFFRACTION100
1.8-1.820.28442820.23165549X-RAY DIFFRACTION100
1.82-1.850.26342530.22375602X-RAY DIFFRACTION100
1.85-1.870.22832870.20365588X-RAY DIFFRACTION100
1.87-1.90.23843270.1965560X-RAY DIFFRACTION100
1.9-1.930.19443090.18235520X-RAY DIFFRACTION100
1.93-1.960.20383070.17635612X-RAY DIFFRACTION100
1.96-1.990.20072930.17645533X-RAY DIFFRACTION100
1.99-2.030.20523050.18445586X-RAY DIFFRACTION100
2.03-2.070.20982870.18595544X-RAY DIFFRACTION100
2.07-2.110.22793270.18155558X-RAY DIFFRACTION100
2.11-2.160.22192770.16475599X-RAY DIFFRACTION100
2.16-2.210.19232300.16165556X-RAY DIFFRACTION100
2.21-2.260.2242960.15995640X-RAY DIFFRACTION100
2.26-2.320.17612530.15765556X-RAY DIFFRACTION100
2.32-2.390.1813170.15515560X-RAY DIFFRACTION100
2.39-2.470.19182750.1575586X-RAY DIFFRACTION100
2.47-2.560.172770.15555572X-RAY DIFFRACTION100
2.56-2.660.18833360.16095551X-RAY DIFFRACTION100
2.66-2.780.20412940.1665516X-RAY DIFFRACTION100
2.78-2.930.1893020.15945517X-RAY DIFFRACTION100
2.93-3.110.20312870.16375555X-RAY DIFFRACTION99
3.11-3.350.19772750.16175559X-RAY DIFFRACTION99
3.35-3.690.16833550.14665374X-RAY DIFFRACTION98
3.69-4.220.17022780.13665532X-RAY DIFFRACTION99
4.22-5.320.16562800.1245552X-RAY DIFFRACTION99
5.32-73.660.17282740.18285520X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.4982-0.2188-0.23910.8475-0.02930.69360.0669-0.04630.06080.183-0.28630.3370.2621-0.3341-0.03630.16640.0001-0.01970.2435-0.05540.2138-42.930114.2863-30.966
21.08920.78750.53642.0035-0.12341.32260.04980.14860.0609-0.1691-0.18510.2343-0.1557-0.1614-0.0010.15160.0572-0.02840.1917-0.05260.1739-41.688926.5584-31.5681
30.47070.35980.26661.1713-0.15450.26280.26180.06060.024-0.2091-0.36910.3655-0.3298-0.1048-0.00630.15360.0385-0.0360.2495-0.0760.2123-45.640420.4407-34.8875
40.37180.109-0.04410.3826-0.08020.35480.1394-0.09530.20140.0493-0.08430.0189-0.2508-0.07-0.00760.18390.0323-0.00340.1687-0.03360.1792-35.184329.3971-26.8271
50.1916-0.51680.00070.8923-0.42420.15160.0797-0.0034-0.03010.0396-0.05120.0696-0.0291-0.062800.1218-0.0086-0.0250.2006-0.01010.1135-36.58498.007-30.5425
60.51-0.12570.2160.8402-0.05320.8014-0.01890.1023-0.01990.0661-0.002-0.00970.06060.004500.0993-0.00890.00840.1546-0.0130.0831-27.8531-4.7258-22.1249
70.904-0.2259-0.2020.4776-0.11340.436-0.03350.21-0.12040.0952-0.06630.01450.2839-0.0641-0.05750.0955-0.02290.00610.1719-0.03270.0873-26.9185-0.1138-27.7909
80.36880.2127-0.06870.16960.15320.7619-0.06060.0471-0.06910.04830.07060.0262-0.078-0.156500.13970.00130.0030.1841-0.01120.1367-29.3453-3.5996-18.3546
91.6770.1826-0.23560.08740.34733.0173-0.0577-0.017-0.5990.03640.13770.42440.6822-0.4617-0.21190.1812-0.10330.00050.29190.00560.2579-33.6396-11.3849-17.2585
100.30050.3865-0.10780.77420.16530.3440.07410.0422-0.1414-0.15070.0356-0.0902-0.0948-0.0133-00.1771-0.00150.04380.20070.03870.2368-15.936725.1701-36.0298
110.43540.3326-0.21420.97330.11280.54740.14850.06920.1367-0.0335-0.033-0.4046-0.2280.13110.01820.2061-0.01530.02620.1626-0.00260.2732-17.45930.267-30.9676
121.5524-0.5863-0.12240.58370.46880.44340.0229-0.25820.1370.44370.0298-0.3489-0.24170.062800.2783-0.0482-0.04730.1871-0.02760.2925-19.711629.2785-24.1864
130.36080.0173-0.22950.5323-0.1080.2434-0.0411-0.02310.20790.27930.0189-0.3951-0.30150.13920.00180.1863-0.0122-0.03590.1501-0.00940.2176-17.207422.9052-25.6734
140.5534-0.117-0.15860.81730.29340.1846-0.01710.3450.10590.06980.05610.4604-0.2412-0.0779-0.00520.2580.04170.04030.20450.08070.2277-28.6533.6522-36.2533
150.1687-0.253-0.10120.28280.03230.1713-0.0784-0.13570.2528-0.09110.0417-0.1779-0.0423-0.00290.00150.103-0.0124-0.02580.1744-0.00740.2204-9.117910.152-26.3473
160.3847-0.30620.1860.4538-0.18930.71350.1968-0.3397-0.37790.2175-0.12290.00990.182-0.2899-0.00160.1281-0.02840.01570.1582-0.00090.1508-25.6052-14.4159-25.1436
171.5210.3089-0.32151.0669-0.67690.8658-0.07860.1503-0.0766-0.20590.0256-0.12380.1406-0.02810.00040.1123-0.0080.0020.1516-0.00890.0907-16.0602-4.621-30.7041
180.3195-0.34210.10350.3608-0.02970.54790.0120.1143-0.2437-0.0735-0.02950.21090.2975-0.2807-0.01280.2346-0.068-0.02150.2167-0.0390.1949-25.2072-16.6738-33.9182
190.38550.01380.49481.17520.34520.6844-0.01640.0352-0.29360.0510.0465-0.25880.29480.0171-0.00010.1686-0.00630.00380.1852-0.02740.1845-12.8784-15.5078-28.343
200.8122-0.2910.51211.19760.27130.4911-0.1572-0.3279-0.08930.2305-0.1712-0.360.05110.6238-0.00210.23150.02190.02480.22350.0020.2254-5.4163-18.9107-60.1323
211.7054-0.0571-0.7482.5154-0.43981.0306-0.06220.009-0.1182-0.0971-0.0782-0.20470.18270.1497-0.01370.18340.05540.04150.12060.02240.1625-7.2043-28.9811-63.0617
221.1141-0.4407-0.09470.2827-0.14610.88750.0369-0.1986-0.09040.2039-0.02920.31980.11250.17-0.00010.22780.05320.0440.15230.00870.1873-14.7266-28.0639-57.944
230.5021-0.3492-0.36720.89620.34411.25880.0414-0.0140.0281-0.0223-0.0101-0.0624-0.0715-0.0408-00.0904-0.01510.00250.1253-0.00050.094-17.74071.1786-55.2661
240.33540.1534-0.07580.1268-0.09581.39640.0278-0.10420.19130.08330.1389-0.2692-0.08850.21990.00430.1158-0.0228-0.00510.1907-0.00910.1559-11.77872.3702-47.839
250.37310.43440.10910.6083-0.14520.4081-0.21540.3216-0.2017-0.08950.06180.11530.1932-0.01960.00080.1678-0.03120.03520.2081-0.08460.2212-33.3376-25.8046-67.2566
260.47160.0415-0.13180.65550.2380.4153-0.21270.3659-0.3363-0.0877-0.03330.25790.2522-0.3173-0.00880.227-0.03010.09820.1137-0.07730.3354-33.0022-31.0351-62.2801
270.6909-0.05190.1474-0.0052-0.04860.3778-0.2138-0.1589-0.04780.35590.2055-0.03430.0312-0.0250.00010.27790.0350.03090.1703-0.00010.3115-27.3168-28.2682-52.5224
280.6604-0.3246-0.17980.4687-0.16320.2556-0.1740.0559-0.34580.08-0.04270.21470.2525-0.1239-0.01340.206-0.01280.09250.1024-0.030.2365-33.7052-28.5062-58.4139
290.49110.3781-0.1051.7754-0.13330.4187-0.54120.2651-0.9680.3680.1227-0.4540.4446-0.0571-0.5790.29260.02470.19490.0841-0.12770.4827-21.6092-35.6255-67.1714
300.2156-0.1158-0.14820.2039-0.05240.09-0.12010.1304-0.1024-0.04330.05150.1320.0586-0.0649-0.00010.1417-0.00320.02310.14010.00030.1704-38.6098-10.8298-57.6134
310.6435-0.1496-0.45080.7294-0.12630.866-0.0931-0.44920.19480.1454-0.0782-0.24-0.03990.308-0.02760.182-0.04590.00350.1526-0.0090.1781-19.475712.8268-55.9463
321.45810.4159-0.37920.9379-0.17591.140.02580.05330.1021-0.0125-0.0260.0124-0.1277-0.00050.00020.09480.00640.00890.0983-0.00680.0824-30.6123.2497-61.1044
330.3239-0.2515-0.17570.25030.25680.3109-0.0210.16310.2828-0.19420.0755-0.2011-0.18610.03650.00020.2076-0.02260.04340.13570.0170.2219-20.355315.1597-64.4095
340.28210.0007-0.33730.3517-0.31870.59670.11340.22380.31930.22580.12140.28-0.273-0.07810.00230.18140.00450.04630.13360.03180.1803-34.055413.7367-59.8667
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 72 )
3X-RAY DIFFRACTION3chain 'H' and (resid 73 through 87 )
4X-RAY DIFFRACTION4chain 'H' and (resid 88 through 100B)
5X-RAY DIFFRACTION5chain 'H' and (resid 100C through 124 )
6X-RAY DIFFRACTION6chain 'H' and (resid 125 through 157 )
7X-RAY DIFFRACTION7chain 'H' and (resid 158 through 175 )
8X-RAY DIFFRACTION8chain 'H' and (resid 176 through 203 )
9X-RAY DIFFRACTION9chain 'H' and (resid 204 through 217 )
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 14 )
11X-RAY DIFFRACTION11chain 'L' and (resid 15 through 38 )
12X-RAY DIFFRACTION12chain 'L' and (resid 39 through 75 )
13X-RAY DIFFRACTION13chain 'L' and (resid 76 through 90 )
14X-RAY DIFFRACTION14chain 'L' and (resid 91 through 101 )
15X-RAY DIFFRACTION15chain 'L' and (resid 102 through 113 )
16X-RAY DIFFRACTION16chain 'L' and (resid 114 through 128 )
17X-RAY DIFFRACTION17chain 'L' and (resid 129 through 174 )
18X-RAY DIFFRACTION18chain 'L' and (resid 175 through 188 )
19X-RAY DIFFRACTION19chain 'L' and (resid 189 through 214 )
20X-RAY DIFFRACTION20chain 'A' and (resid 1 through 17 )
21X-RAY DIFFRACTION21chain 'A' and (resid 18 through 87 )
22X-RAY DIFFRACTION22chain 'A' and (resid 88 through 111 )
23X-RAY DIFFRACTION23chain 'A' and (resid 112 through 188 )
24X-RAY DIFFRACTION24chain 'A' and (resid 189 through 214 )
25X-RAY DIFFRACTION25chain 'B' and (resid 1 through 14 )
26X-RAY DIFFRACTION26chain 'B' and (resid 15 through 38 )
27X-RAY DIFFRACTION27chain 'B' and (resid 39 through 61 )
28X-RAY DIFFRACTION28chain 'B' and (resid 62 through 90 )
29X-RAY DIFFRACTION29chain 'B' and (resid 91 through 101 )
30X-RAY DIFFRACTION30chain 'B' and (resid 102 through 113 )
31X-RAY DIFFRACTION31chain 'B' and (resid 114 through 128 )
32X-RAY DIFFRACTION32chain 'B' and (resid 129 through 174 )
33X-RAY DIFFRACTION33chain 'B' and (resid 175 through 188 )
34X-RAY DIFFRACTION34chain 'B' and (resid 189 through 211 )

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