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- PDB-9puk: Neutralizing monoclonal antibody Fab fragment for human leptin -

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Basic information

Entry
Database: PDB / ID: 9puk
TitleNeutralizing monoclonal antibody Fab fragment for human leptin
Components
  • Neutralizing monoclonal antibody Fab fragment for human leptin, heavy chain
  • Neutralizing monoclonal antibody Fab fragment for human leptin, light chain
KeywordsIMMUNE SYSTEM / Antibody / FAB / leptin
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsTomchick, D.R. / Wynn, R.M. / Scherer, P.E.
Funding support United States, 12items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK55758 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK099110 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK118620 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK127274 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK131537 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG051459 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK138935 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG084646 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP220032 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP150551 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP190561 United States
Robert A. Welch FoundationAU-0042-20030616 United States
CitationJournal: Sci Adv / Year: 2025
Title: Leptin as a key driver for organ fibrogenesis.
Authors: Sun, X.N. / Chen, S. / Zhao, S. / Funcke, J.B. / Virostek, M. / Pedersen, L. / Li, C. / Joung, C. / Lin, Q. / Li, Y. / Cobb, A. / Wang, M.Y. / Min, K. / Maya-Ramos, L. / Degasperi, G. / Liu, ...Authors: Sun, X.N. / Chen, S. / Zhao, S. / Funcke, J.B. / Virostek, M. / Pedersen, L. / Li, C. / Joung, C. / Lin, Q. / Li, Y. / Cobb, A. / Wang, M.Y. / Min, K. / Maya-Ramos, L. / Degasperi, G. / Liu, J. / Zhang, N. / An, Z. / Tomchick, D.R. / Wynn, R.M. / Oh, D.Y. / Scherer, P.E.
History
DepositionJul 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neutralizing monoclonal antibody Fab fragment for human leptin, heavy chain
B: Neutralizing monoclonal antibody Fab fragment for human leptin, light chain
C: Neutralizing monoclonal antibody Fab fragment for human leptin, heavy chain
D: Neutralizing monoclonal antibody Fab fragment for human leptin, light chain


Theoretical massNumber of molelcules
Total (without water)93,2304
Polymers93,2304
Non-polymers00
Water00
1
A: Neutralizing monoclonal antibody Fab fragment for human leptin, heavy chain
B: Neutralizing monoclonal antibody Fab fragment for human leptin, light chain


Theoretical massNumber of molelcules
Total (without water)46,6152
Polymers46,6152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Neutralizing monoclonal antibody Fab fragment for human leptin, heavy chain
D: Neutralizing monoclonal antibody Fab fragment for human leptin, light chain


Theoretical massNumber of molelcules
Total (without water)46,6152
Polymers46,6152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.215, 207.941, 72.823
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 100 or resid 108 through 222))
d_2ens_1(chain "C" and (resid 2 through 100 or resid 108 through 135 or resid 143 through 222))
d_1ens_2chain "B"
d_2ens_2(chain "D" and (resid 3 through 57 or resid 60 through 213))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1VALVALGLNGLNAA2 - 1002 - 100
d_12ens_1GLYGLYPROPROAA108 - 222108 - 222
d_21ens_1VALVALGLNGLNCC2 - 1002 - 100
d_22ens_1GLYGLYPROPROCC108 - 135108 - 135
d_23ens_1GLYGLYPROPROCC143 - 222143 - 222
d_11ens_2VALVALPROPROBB3 - 2133 - 213
d_21ens_2VALVALPROPRODD3 - 573 - 57
d_22ens_2VALVALPROPRODD60 - 21360 - 213

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.992497180184, 0.108854989817, 0.0556770915051), (0.110512226648, 0.993491525363, 0.0275977678845), (-0.0523105638252, 0.0335437061603, -0.998067344767)1.03644913573, -4.90385791909, -36.9077858336
2given(-0.994461746271, 0.0893928992679, 0.0552697454718), (0.0910460491201, 0.995448782753, 0.0281484964833), (-0.0525019251423, 0.0330246949288, -0.998074605118)1.82679494419, -4.59994502285, -37.1730014588

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Components

#1: Antibody Neutralizing monoclonal antibody Fab fragment for human leptin, heavy chain


Mass: 23681.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody Neutralizing monoclonal antibody Fab fragment for human leptin, light chain


Mass: 22933.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Fab at 25 mg/ml in 20 mM Hepes, pH 7.4, 75 mM NaCl versus 1.0 M lithium chloride, 0.1 M citrate pH 4.0, 20% (w/v) PEG 6,000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 17545 / % possible obs: 100 % / Redundancy: 21.4 % / Biso Wilson estimate: 47.74 Å2 / CC1/2: 0.68 / CC star: 0.9 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.036 / Rrim(I) all: 0.168 / Net I/σ(I): 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.25-3.317.61.4398710.680.90.5241.5380.89699.9
3.31-3.3711.11.4638590.860.9620.4411.5310.898100
3.37-3.43141.418450.80.9430.3761.4610.945100
3.43-3.517.41.318690.8990.9730.3151.3481.001100
3.5-3.58201.1058390.9160.9780.2491.1330.917100
3.58-3.6621.61.0028740.9310.9820.2181.0260.995100
3.66-3.7522.80.8898490.9420.9850.1880.911.026100
3.75-3.8523.20.7098770.9610.990.1490.7250.912100
3.85-3.9722.60.6298530.9710.9930.1340.6431.218100
3.97-4.0921.80.3988620.9830.9960.0860.4080.907100
4.09-4.2425.70.3148760.9910.9980.0630.320.906100
4.24-4.4125.50.2238770.9960.9990.0450.2280.941100
4.41-4.6125.40.2018730.9940.9990.040.2060.94100
4.61-4.8525.10.1748690.9950.9990.0350.1780.948100
4.85-5.1624.60.1518630.9970.9990.0310.1540.928100
5.16-5.5623.30.1428910.9950.9990.030.1450.898100
5.56-6.1125.80.1328940.9960.9990.0260.1350.849100
6.11-725.20.1098980.9970.9990.0220.1110.803100
7-8.8122.80.0719220.99910.0150.0730.719100
8.81-5022.20.0619840.9960.9990.0140.0620.737100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-3000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→49.33 Å / SU ML: 0.4782 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.0181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3195 1576 10.05 %
Rwork0.2674 14107 -
obs0.2726 15683 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.28 Å2
Refinement stepCycle: LAST / Resolution: 3.3→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6250 0 0 0 6250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226400
X-RAY DIFFRACTIONf_angle_d0.53648718
X-RAY DIFFRACTIONf_chiral_restr0.0463984
X-RAY DIFFRACTIONf_plane_restr0.00531114
X-RAY DIFFRACTIONf_dihedral_angle_d11.80152258
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.71430244615
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.798700610301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.410.3823610.3157592X-RAY DIFFRACTION44.73
3.41-3.530.35421370.30171162X-RAY DIFFRACTION86.77
3.53-3.670.36441450.29331349X-RAY DIFFRACTION99.73
3.67-3.840.35711560.27641327X-RAY DIFFRACTION100
3.84-4.040.29181440.26711360X-RAY DIFFRACTION100
4.04-4.290.29541500.24331343X-RAY DIFFRACTION100
4.29-4.620.27921530.22851366X-RAY DIFFRACTION100
4.62-5.090.28871510.22931359X-RAY DIFFRACTION99.93
5.09-5.820.28681550.25771375X-RAY DIFFRACTION99.93
5.82-7.330.36551550.29961399X-RAY DIFFRACTION100
7.33-49.330.32461690.28311475X-RAY DIFFRACTION99.7
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9264964568990.1832687968190.07624627609842.046671733370.2015595180981.5127204688-0.4533381931140.887937595928-0.380946859421-0.4266307151150.01073090988630.1104626916770.158960250691-0.05811382047650.2163298419360.6251281481820.00846067047564-0.05965098965960.608528415987-0.06183886299140.70818550034814.624355106721.3031000208-26.5765702774
20.268279878221-0.55000814965-0.1142390844231.54381062123-0.2086252156190.3761708490360.1150193325720.0729378284399-0.238933016459-0.3397914632630.3639800830.588688670321-0.54650844013-0.309291565028-0.09999774711040.5552493569550.0852132589825-0.1024769527780.4539815947640.08220365633540.35232592995716.255829938129.7756403973-22.7839094462
30.535631050693-0.0802996886559-0.288055859290.3883769429590.1539850135140.5517008866360.00186262123676-0.2995613976410.3350723129960.4898980289090.00597620086272-0.0823048490164-0.162939335671-0.193712168546-0.181392015148-0.629803465901-0.1239541318240.4507203650981.293474887570.314003269190.27970067097221.498229363654.9362637185-13.4355830621
42.187363065030.199425254017-0.09208395688272.222880204270.4726164458411.043610231940.00558593803709-0.313406812922-0.1552479189690.2458186883170.262241639290.4295110499010.3611553801760.350071883987-0.07281573319790.4206620105480.0355053251906-0.08022595910760.3643551088560.1530840862060.26451392402520.94652522545.8690235008-14.8702020407
52.335109887210.6339697303631.085129371311.44567023770.2158587441022.192128772580.00930125698748-0.2460142759950.787719456523-0.00751790709271-0.3566973072660.292259061985-0.5620598622160.2851129224910.1631939535020.312926164118-0.07462769565410.02920797659110.7014571426580.02985614395050.36937849885627.289251129752.5138849998-16.5323636132
60.8364674350080.3860841354510.1578327571650.3741454926280.2589695041151.03377353914-0.354967424377-0.226324525818-0.4404565771520.4141928208780.2327847593341.10907302740.2009993631840.3880679511070.08152293043850.851785573812-0.05535885195590.06065699670750.590489765571-0.02623824083281.0002218844917.628364180216.1454057637-4.08589258512
70.406215706231-0.154573085348-0.3269959535320.06311031992020.126923458870.257482003961-0.1145688054080.494128792596-0.918468221231-0.0171101344732-0.03929352558630.219211807740.518082698987-0.458377623573-0.02578902428291.268140775360.176619717615-0.5444026583391.56418654201-0.2869490017771.2788198954928.93818267512.3292094735-5.27585223008
80.315693311310.286081692005-0.1486607876981.03662398923-0.5496741690690.297513418322-0.260340221231-0.2066857755810.06116151720440.3743394594930.139602634845-0.398094026450.102046249701-0.146074945051-0.1960440947321.178931172530.113342540492-0.329333069234-0.007682488122840.261357725261.5279210281920.161719339210.4252876324-0.00277053689711
90.484920313496-0.710563703492-0.81460500051.883570166260.2604222658052.27078221756-0.378173812542-0.27658696209-0.624938915280.2397498658570.06841307003081.055595173830.083861163568-0.3446072476680.1512337932630.550810297417-0.06252548592520.1098318762330.343881909474-0.1102510633110.79894695855216.355927423616.5361399147-7.98135574735
103.62066633479-1.50859282092-2.426372262012.710692762760.02405483487642.08781944219-0.662648056804-0.139246937786-0.67731758264-0.139904675232-0.3825963510530.1055399720860.620620657998-0.05209645652910.1645041483010.5125298666640.025977121096-0.02227474967230.740030855490.120182066330.37883582996919.520819778533.2954336045.2992956293
110.640658793782-0.5723361515390.6398338317233.78482562657-0.8401662886910.6463408950810.5278856742140.9525410703070.357625078234-1.20987451018-0.4024540257910.474093713903-0.649859990435-0.444023353368-0.1183450572550.6812209533080.5687628190830.2334064828090.7580665988440.3666586132690.54325816216516.619095872160.7840872948-11.9088604222
122.594019225260.243190397877-0.7389059158222.004150217120.02361075357970.9615889487630.1661098364280.7568360224840.3258235136650.8057493425810.007736995255370.2626569199250.354206304612-0.672097982625-0.05522220834380.60314295457-0.07567342508570.03009172695940.6655170586340.0386148822570.28565221095713.824483098649.6192927056-0.240878304464
130.9449927841350.5775639226810.6698571655421.308076165631.0244394080.961729168023-0.08141899494260.729995347625-0.3491422426640.3098396261170.368015229410.216451551050.387576342298-0.675713964630.2195136443860.5202398116890.1260194501260.2217852232630.8854731543070.04114694426210.37447531027511.738150278347.2490692618-2.51858589081
142.326150888610.903334153975-1.780779946851.040784594640.3416392229312.84581982170.41839838121-0.1693577660130.6061477345660.2187013085120.1843845465760.0921228954464-1.17540530075-1.035063162610.2366882758281.064250306650.196507920776-0.1377332550510.697539985309-0.00273074552580.2661764128310.392539600158.3595096242-8.19562517407
152.366423298190.256178795954-0.5373474528313.05354781899-1.181649754271.300561294220.362367372601-0.1007642422860.4999013268270.318939948802-0.205998691770.326355528438-0.655290440586-1.46306740525-0.03827466703921.054670292110.1371526191060.02614211014860.859102369196-0.2562810295930.319969563912.471362314757.57908667823.38344031275
161.713793970560.3876441338970.7550762311910.7314074932841.06976509132.61612928640.0397017188611-1.46933304525-1.137070851840.203968389619-0.223925084723-0.4728673176070.78430646858-1.53162131423-0.7138534796560.713979203182-0.239481890064-0.2373919546050.8261617479640.4580405100480.805402531375-12.962661757818.6483743675-11.4498568912
172.45587219108-0.7296589308250.2763234870471.450732730940.7558051313741.89941665095-0.0420139086646-0.2294674996450.1959140715560.133138463940.2124995440210.2378045212540.0952437842602-0.628988238046-0.04086646629950.1338073839660.03831893380510.02887561602060.3500217790430.09582717330350.211987932725-18.1039914448.5473131548-22.0001537156
180.61101341916-0.337765058784-0.09563579528390.2080683982030.1162688168740.817549600576-0.4767619049430.439925210815-0.446869235758-0.9943692768430.5659905787690.06338253668750.1205545992950.0661526298989-0.05236533630680.803330901209-0.1439642010150.06906530757110.272664303780.003410967339581.00084493827-17.087894321612.5984344417-33.8541519554
190.6346856253490.331141220304-0.3057609847360.3050244660210.05179128048390.419866941745-0.178202196857-0.0688137385094-0.6872902044740.06653347300010.0668033564543-0.7190571271090.6773113022370.182392222085-0.1873792081790.886835542872-0.1460973342770.007045386783240.236979875382-0.1646582728390.651592110971-10.917134339617.9264862222-32.4477396318
202.367953445230.0218292409916-0.2531476732982.01863725715-0.2503419351973.36039458252-0.0381371791244-0.474050897319-0.08097876099260.259550449756-0.0202312385936-0.3757070895010.6736049155980.364747890629-0.03225434555090.15462006146-0.0841447527468-0.1063082285240.189878117979-0.1462386660220.163186611241-6.4984590185849.7703672734-30.8544760626
211.36979493517-0.739938759044-0.230311234092.561535127710.4119600328542.217848821620.196520913846-0.07406923422370.360795915632-0.963004557772-0.173579053859-0.52467628812-0.2472314705170.741981403671-0.03818044497050.367517265327-0.1034486040170.1320184972510.1303689056050.2593147140010.0991986966603-5.5789446048154.0987955713-39.401465129
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 99 )AA2 - 991 - 98
22chain 'A' and (resid 100 through 128 )AA100 - 12899 - 121
33chain 'A' and (resid 129 through 154 )AA129 - 154122 - 140
44chain 'A' and (resid 155 through 184 )AA155 - 184141 - 170
55chain 'A' and (resid 185 through 222 )AA185 - 222171 - 208
66chain 'B' and (resid 3 through 50 )BB3 - 501 - 48
77chain 'B' and (resid 51 through 63 )BB51 - 6349 - 59
88chain 'B' and (resid 64 through 77 )BB64 - 7760 - 73
99chain 'B' and (resid 78 through 105 )BB78 - 10574 - 101
1010chain 'B' and (resid 106 through 118 )BB106 - 118102 - 112
1111chain 'B' and (resid 119 through 134 )BB119 - 134113 - 128
1212chain 'B' and (resid 135 through 155 )BB135 - 155129 - 149
1313chain 'B' and (resid 156 through 176 )BB156 - 176150 - 170
1414chain 'B' and (resid 177 through 192 )BB177 - 192171 - 186
1515chain 'B' and (resid 193 through 213 )BB193 - 213187 - 207
1616chain 'C' and (resid 2 through 128 )CC2 - 1281 - 122
1717chain 'C' and (resid 129 through 223 )CC129 - 223123 - 217
1818chain 'D' and (resid 2 through 94 )DD2 - 941 - 93
1919chain 'D' and (resid 95 through 118 )DD95 - 11894 - 115
2020chain 'D' and (resid 119 through 192 )DD119 - 192116 - 189
2121chain 'D' and (resid 193 through 213 )DD193 - 213190 - 210

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