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- PDB-9d97: KIR3DL1 - HLA-B*38-YHE complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9d97
TitleKIR3DL1 - HLA-B*38-YHE complex
Components
  • Beta-2-microglobulin
  • Cyclin-A2
  • Killer cell immunoglobulin-like receptor 3DL1
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Killer Immunoglobulin-like receptor / Human Leucocyte Antigen / immune complex / NK cell
Function / homology
Function and homology information


HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / G2/M DNA replication checkpoint / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus ...HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / G2/M DNA replication checkpoint / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of DNA biosynthetic process / natural killer cell mediated cytotoxicity / cellular response to insulin-like growth factor stimulus / cyclin A2-CDK2 complex / G2 Phase / p53-Dependent G1 DNA Damage Response / Regulation of APC/C activators between G1/S and early anaphase / regulation of DNA replication / microtubule organizing center / G0 and Early G1 / cochlea development / Telomere Extension By Telomerase / animal organ regeneration / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / antigen processing and presentation of peptide antigen via MHC class I / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / Cyclin A/B1/B2 associated events during G2/M transition / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / cellular response to platelet-derived growth factor stimulus / cellular response to nitric oxide / post-translational protein modification / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to estradiol stimulus / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / response to molecule of bacterial origin / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / G1/S transition of mitotic cell cycle / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / G2/M transition of mitotic cell cycle / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / positive regulation of fibroblast proliferation / SCF(Skp2)-mediated degradation of p27/p21 / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Orc1 removal from chromatin / Modulation by Mtb of host immune system / positive regulation of cellular senescence / sensory perception of smell / tertiary granule lumen / MHC class II protein complex binding / Regulation of TP53 Degradation / DAP12 signaling / T cell differentiation in thymus / late endosome membrane / negative regulation of neuron projection development / protein refolding / ER-Phagosome pathway / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / early endosome membrane
Similarity search - Function
: / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C ...: / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Immunoglobulin / Immunoglobulin domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / Cyclin-A2 / Killer cell immunoglobulin-like receptor 3DL1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhu, S. / Vivian, J. / Petersen, J. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: The ancient MHC class I molecule HLA-B*38:01 calibrates the immune system to protect against multiple sclerosis
Authors: Ladell, K. / Zhu, S. / Kaufmann, M. / Vivian, J. / Petersen, J. / Rossjohn, J. / Price, D. / Fugger, L.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Data collection / Category: diffrn_radiation_wavelength / diffrn_source
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Cyclin-A2
G: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9857
Polymers78,3224
Non-polymers6643
Water10,287571
1
G: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules

A: MHC class I antigen
B: Beta-2-microglobulin
C: Cyclin-A2


Theoretical massNumber of molelcules
Total (without water)78,9857
Polymers78,3224
Non-polymers6643
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Buried area7180 Å2
ΔGint-21 kcal/mol
Surface area31920 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-21 kcal/mol
Surface area31790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.963, 60.047, 63.337
Angle α, β, γ (deg.)94.960, 95.500, 106.230
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 3 types, 3 molecules ABG

#1: Protein MHC class I antigen / MHC class II antigen


Mass: 32029.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLA-DRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: E5FQ58
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#4: Protein Killer cell immunoglobulin-like receptor 3DL1 / CD158 antigen-like family member E / HLA-BW4-specific inhibitory NK cell receptor / Natural killer- ...CD158 antigen-like family member E / HLA-BW4-specific inhibitory NK cell receptor / Natural killer-associated transcript 3 / NKAT-3 / p70 natural killer cell receptor clones CL-2/CL-11 / p70 NK receptor CL-2/CL-11


Mass: 33220.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR3DL1, CD158E, NKAT3, NKB1 / Production host: Homo sapiens (human) / References: UniProt: P43629

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Protein/peptide / Sugars / Non-polymers , 3 types, 575 molecules C

#3: Protein/peptide Cyclin-A2 / Cyclin-A / Cyclin A


Mass: 1192.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Production host: synthetic construct (others) / References: UniProt: P20248
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 3350, 2% Tacsimate, pH 5.0, 0.1 M Na3citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95368 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95368 Å / Relative weight: 1
ReflectionResolution: 1.6→44.74 Å / Num. obs: 84176 / % possible obs: 96.16 % / Redundancy: 4.1 % / CC1/2: 0.995 / CC star: 0.999 / Rpim(I) all: 0.05153 / Net I/σ(I): 8.61
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.48 / Num. unique obs: 8259 / CC1/2: 0.531 / CC star: 0.833 / Rpim(I) all: 0.4862 / % possible all: 95.49

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→44.74 Å / SU ML: 0.163 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 19.7776
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1948 2000 2.4 %
Rwork0.1643 81332 -
obs0.1651 83332 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5333 0 42 571 5946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00585558
X-RAY DIFFRACTIONf_angle_d0.83027578
X-RAY DIFFRACTIONf_chiral_restr0.0559802
X-RAY DIFFRACTIONf_plane_restr0.0074990
X-RAY DIFFRACTIONf_dihedral_angle_d13.52642004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.24591410.23265737X-RAY DIFFRACTION95.42
1.64-1.680.29821420.22095799X-RAY DIFFRACTION95.65
1.68-1.730.2261430.21565789X-RAY DIFFRACTION95.77
1.73-1.790.23481420.19825793X-RAY DIFFRACTION95.86
1.79-1.850.21581430.19365805X-RAY DIFFRACTION96.15
1.85-1.930.17561430.17195819X-RAY DIFFRACTION96.41
1.93-2.020.19641440.15925849X-RAY DIFFRACTION96.77
2.02-2.120.17551440.15615858X-RAY DIFFRACTION96.98
2.12-2.260.20831460.16365917X-RAY DIFFRACTION97.48
2.26-2.430.21361450.16675876X-RAY DIFFRACTION97.6
2.43-2.670.20531440.17865880X-RAY DIFFRACTION97.49
2.67-3.060.21761420.17435816X-RAY DIFFRACTION96.24
3.06-3.860.17381400.14775667X-RAY DIFFRACTION93.89
3.86-44.740.17011410.14415727X-RAY DIFFRACTION94.49
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)
12.54239595783-0.8225640821061.726941724881.3568392711-0.3007156458982.068829711220.1753331944980.0634854407001-0.284518822197-0.05133165816090.0571455729534-0.142653622550.03797959034860.164823629472-0.2135691878270.1633459233570.00813202057291-0.004640114374630.15526750011-0.01611618739930.1720940989258.95276253099-7.88398989617-19.1048395495
20.666808087112-1.45513673351.384440234269.377433475311.931183229796.82824479263-0.0383053938271-0.0836944168783-0.3009303785420.4604385576130.167916271239-0.36188546078-0.05364153724970.155377482458-0.1146352956950.6001349106540.0393276451256-0.2606350743680.542700501574-0.02203429374580.51520088018225.44279258-12.2757367924-0.974550846666
30.4275497732160.1161563867330.696540724090.858584410714-0.1911813362421.3092746157-0.0712209967145-0.124350411040.0394362887486-0.04715601681690.01876435299860.160763116248-0.181035492918-0.06294175246350.06413242413750.1864366089760.0511666636251-0.03240229329470.202612042756-0.04310562494460.1685176076659.666523174580.637215618866-7.09036748238
43.8406636553-2.35092146625-0.01179875099026.70789963506-0.2252724970972.400992350160.0433936439285-0.491806474359-0.3645014111720.3873123084360.1160581109790.1538924413920.430849682253-0.101646725471-0.1873758514480.2920347467350.023669095848-0.04690114354230.2561218037060.02085537970780.22614277108613.8448573139-12.4753816799-2.76151350884
51.98813421179-2.9170698513-0.6493163583614.59420424661.146441724980.3309345418260.2552714751990.326232139183-0.0162495322451-0.507674841392-0.2229549935470.197729087638-0.20960612684-0.136357715865-0.01783497411510.223174771922-0.03129905771760.006923626166920.2265114456350.02702132130730.171480879662-2.5861619242-1.70410461607-40.658767087
61.42474227830.4290412896310.9333870873571.107060951370.007294880531451.198859255940.133209112637-0.248571787515-0.1292525908040.264510880327-0.118365086136-0.1793193688520.06255678639050.01300666732770.01976313861350.215562332407-0.0300088859245-0.01067607814260.228120464210.006229896861180.20093453199513.763499604925.6095296064-24.9665111902
72.32085645080.851960181137-0.0005524993930622.290811511720.3119175359851.016697736940.02749259755240.03781314087910.0240487623703-0.09762868789030.00635495559236-0.209344686676-0.0543106334950.0990598737631-0.05111016118110.1590230114520.01319763112090.01958279377450.1592715050190.001165398957680.1426077033644.1390642575221.9866470249-48.9685977277
80.6357063541790.1980329661620.7315444902831.149096865610.3491344587151.42504220464-0.06270573828380.03572406792340.0189063109728-0.107890739530.0573800083444-0.0969060608279-0.1265874686320.1052840129840.007828198111690.1432938105580.0001591744695520.0348008712740.160176114208-0.009126213633560.152711325763-3.4346411363722.0633132899-45.9188883253
91.98297555849-0.232006240061-0.2543814374671.695685715150.3653145163581.856724098370.1342643060050.007671331471020.133776311799-0.103751799533-0.03135691229530.208254624448-0.265388856609-0.129679888138-0.07007027593720.1892946837940.0141201190540.01032392382510.1986724611760.02142900867910.193815335177-25.485813792613.2110794378-52.3613412564
101.63200517935-0.671077284555-0.4081581019281.540575760530.1005315062861.050506718880.004457201965610.004377130947460.0336337569091-0.06748633623970.0665713414811-0.08831101530410.007086063848750.0204537557179-0.06750257633640.129341913057-0.0172657269894-0.004553056605550.1232227470537.90003882898E-50.12668377152.76414364168-3.35434976135-32.9620793825
111.35887166723-0.6910432643140.2898333559660.665329857321-0.392140216890.6925742389010.09286046263140.103495240437-0.197476648239-0.117733841524-0.04591912013870.215759892990.0956965921864-0.203253802199-0.05767866897630.162245823725-0.0390610644765-0.01588750418750.1757493626140.01107108546310.196968825145-9.38190096377-7.76656443821-37.1954156376
120.9063998081630.17442753766-0.4323226001551.23847328299-0.2840433241922.769362086630.0138981055837-0.171134596863-0.00748087551620.134502472010.03539082957930.0926066389820.281936833990.0275226224145-0.05673906166290.2086809577430.0149888183774-9.44080767252E-50.1840431635450.0006158209651150.1848571909955.08528944574-27.7545311045-8.90902549212
139.52635740602-4.18304420374.884152970647.15150143197-3.050043704396.749747254330.1863110881880.008315825164920.382645536286-0.332149806430.02049052941890.605344048998-0.178902930829-0.471757063634-0.1836450600820.2192881399370.0860438891703-0.001484618848350.2778899672880.02521713757910.238954565314-3.508318679780.573105866538-13.0367839087
142.48879525374-0.9496762333780.7610353711742.02586497613-0.5996736058041.40120873314-0.04988057543680.115575547728-0.3655519943730.2079225131230.150198480894-0.1755872283530.1092797309970.186148300263-0.07112259294190.1755953715080.0430829681709-0.04425121846530.171083125971-0.05209803661060.20407383693715.0743121096-13.9047174368-11.5164498422
158.6882034133-1.342824514734.650139059351.0078260472-0.8626640436143.38264366223-0.1549783825960.2895860861390.4521546987080.07013973730380.0373253195044-0.217647943519-0.09431649648020.3406659299320.1015153407390.1729631928040.00853997119157-0.01169032473660.192512674515-0.006352580805070.16855242356311.026015453-0.610914864666-13.046407545
163.067615706260.7205054152652.566431768562.161337191470.9136219788882.28301235851-0.1707983811140.4096462316420.120728037273-0.1752979212120.51363083971-0.38059046667-0.4605698938350.906972687427-0.3335895633130.253894537953-0.08290900984220.006595274653520.376438292081-0.03664884137510.24380004312422.1029217253-2.621230641-12.1181111138
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 52 through 71 )BB52 - 7153 - 72
22chain 'B' and (resid 72 through 77 )BB72 - 7773 - 78
33chain 'B' and (resid 78 through 90 )BB78 - 9079 - 91
44chain 'B' and (resid 91 through 99 )BB91 - 9992 - 100
55chain 'C' and (resid 1 through 9 )CC1 - 91 - 9
66chain 'G' and (resid 6 through 108 )GD6 - 1081 - 103
77chain 'G' and (resid 109 through 169 )GD109 - 169104 - 164
88chain 'G' and (resid 170 through 208 )GD170 - 208165 - 203
99chain 'G' and (resid 209 through 294 )GD209 - 294204 - 289
1010chain 'A' and (resid 1 through 118 )AA1 - 1181 - 118
1111chain 'A' and (resid 119 through 174 )AA119 - 174119 - 174
1212chain 'A' and (resid 175 through 276 )AA175 - 276175 - 276
1313chain 'B' and (resid 0 through 5 )BB0 - 51 - 6
1414chain 'B' and (resid 6 through 30 )BB6 - 307 - 31
1515chain 'B' and (resid 31 through 41 )BB31 - 4132 - 42
1616chain 'B' and (resid 42 through 51 )BB42 - 5143 - 52

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