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- PDB-7zmk: Structure of human MFAP4 in complex with the Fab fragment of the ... -

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Basic information

Entry
Database: PDB / ID: 7zmk
TitleStructure of human MFAP4 in complex with the Fab fragment of the AS0326 monoclonal antibody
Components
  • Light chain of AS0326
  • Microfibril-associated glycoprotein 4
  • heavy chain of antibody AS0326
KeywordsCELL ADHESION / antibody / MFAP4 / extracellular matrix
Function / homology
Function and homology information


regulation of collagen metabolic process / elastic fiber / microfibril / elastic fiber assembly / UV protection / Molecules associated with elastic fibres / cellular response to UV-B / supramolecular fiber organization / collagen-containing extracellular matrix / cell adhesion ...regulation of collagen metabolic process / elastic fiber / microfibril / elastic fiber assembly / UV protection / Molecules associated with elastic fibres / cellular response to UV-B / supramolecular fiber organization / collagen-containing extracellular matrix / cell adhesion / extracellular space / extracellular region
Similarity search - Function
Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile.
Similarity search - Domain/homology
Microfibril-associated glycoprotein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLaursen, N.S. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: To Be Published
Title: MFAP4-targeted immunotherapy inhibits retinal neovascularization and vascular leakage
Authors: Pilecki, B.
History
DepositionApr 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microfibril-associated glycoprotein 4
B: heavy chain of antibody AS0326
C: Light chain of AS0326
D: Microfibril-associated glycoprotein 4
E: heavy chain of antibody AS0326
F: Light chain of AS0326
G: heavy chain of antibody AS0326
H: Light chain of AS0326
I: Microfibril-associated glycoprotein 4
J: heavy chain of antibody AS0326
K: Light chain of AS0326
L: Microfibril-associated glycoprotein 4
M: heavy chain of antibody AS0326
N: Light chain of AS0326
O: Microfibril-associated glycoprotein 4
P: heavy chain of antibody AS0326
Q: Light chain of AS0326
R: Microfibril-associated glycoprotein 4
S: heavy chain of antibody AS0326
T: Light chain of AS0326
U: Microfibril-associated glycoprotein 4
V: heavy chain of antibody AS0326
W: Light chain of AS0326
X: Microfibril-associated glycoprotein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)611,83632
Polymers611,51624
Non-polymers3218
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Not verified in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)317.320, 126.600, 187.550
Angle α, β, γ (deg.)90.000, 98.857, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
12
22
32
42
52
62
72
82
13
23
33
43
53
63
73
83

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNALAALA(chain 'A' and resid 16 through 501)AA16 - 23437 - 255
221GLNGLNALAALA(chain 'D' and resid 16 through 501)DD16 - 23437 - 255
331GLNGLNALAALAchain 'I'II16 - 23437 - 255
441GLNGLNALAALA(chain 'L' and resid 16 through 501)LL16 - 23437 - 255
551GLNGLNALAALA(chain 'O' and resid 16 through 501)OO16 - 23437 - 255
661GLNGLNALAALAchain 'R'RR16 - 23437 - 255
771GLNGLNALAALA(chain 'U' and resid 16 through 501)UU16 - 23437 - 255
881GLNGLNALAALA(chain 'X' and resid 16 through 501)XX16 - 23437 - 255
192GLNGLNVALVAL(chain 'B' and resid 1 through 221)BB1 - 2201 - 220
2102GLNGLNVALVAL(chain 'E' and resid 1 through 221)EE1 - 2201 - 220
3112GLNGLNVALVAL(chain 'G' and resid 1 through 221)GG1 - 2201 - 220
4122GLNGLNVALVAL(chain 'J' and resid 1 through 221)JJ1 - 2201 - 220
5132GLNGLNVALVALchain 'M'MM1 - 2201 - 220
6142GLNGLNVALVAL(chain 'P' and resid 1 through 221)PP1 - 2201 - 220
7152GLNGLNVALVAL(chain 'S' and resid 1 through 221)SS1 - 2201 - 220
8162GLNGLNVALVALchain 'V'VV1 - 2201 - 220
1173ASPASPGLUGLUchain 'C'CC1 - 2131 - 213
2183ASPASPGLUGLUchain 'F'FF1 - 2131 - 213
3193ASPASPGLUGLUchain 'H'HH1 - 2131 - 213
4203ASPASPGLUGLUchain 'K'KK1 - 2131 - 213
5213ASPASPGLUGLUchain 'N'NN1 - 2131 - 213
6223ASPASPGLUGLUchain 'Q'QQ1 - 2131 - 213
7233ASPASPGLUGLUchain 'T'TT1 - 2131 - 213
8243ASPASPGLUGLUchain 'W'WW1 - 2131 - 213

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Microfibril-associated glycoprotein 4


Mass: 28674.162 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MFAP4 / Production host: Homo sapiens (human) / References: UniProt: P55083
#2: Antibody
heavy chain of antibody AS0326


Mass: 24295.252 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody
Light chain of AS0326


Mass: 23470.064 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: H2O
Has ligand of interestN

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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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion
Details: 0.14 M Ammonium phosphate dibasic, 14 % w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.041 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.041 Å / Relative weight: 1
ReflectionResolution: 3.4→49.25 Å / Num. obs: 100955 / % possible obs: 99.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 101.68 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.233 / Net I/σ(I): 5.3
Reflection shellResolution: 3.4→3.52 Å / Num. unique obs: 9948 / CC1/2: 0.472 / Rsym value: 1.542

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M7H, 4JPI

4m7h

4jpi


Resolution: 3.4→48.85 Å / SU ML: 0.5205 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.3754
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.277 1997 1.98 %
Rwork0.2393 98845 -
obs0.2401 100842 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 132.39 Å2
Refinement stepCycle: LAST / Resolution: 3.4→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41000 0 0 16 41016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005142070
X-RAY DIFFRACTIONf_angle_d0.898757092
X-RAY DIFFRACTIONf_chiral_restr0.04936084
X-RAY DIFFRACTIONf_plane_restr0.00537340
X-RAY DIFFRACTIONf_dihedral_angle_d5.396924572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.480.49431410.40786956X-RAY DIFFRACTION98.6
3.48-3.580.39461400.37826983X-RAY DIFFRACTION99.72
3.58-3.680.40741420.35717029X-RAY DIFFRACTION99.71
3.68-3.80.39841420.31297055X-RAY DIFFRACTION99.83
3.8-3.940.29761430.2827024X-RAY DIFFRACTION99.72
3.94-4.10.28161420.26157017X-RAY DIFFRACTION99.6
4.1-4.280.28051420.24857059X-RAY DIFFRACTION99.88
4.28-4.510.19531430.20377051X-RAY DIFFRACTION99.83
4.51-4.790.23421420.19057038X-RAY DIFFRACTION99.86
4.79-5.160.24281430.19677086X-RAY DIFFRACTION99.93
5.16-5.680.27711440.21297071X-RAY DIFFRACTION99.88
5.68-6.50.26021430.23027116X-RAY DIFFRACTION99.97
6.5-8.180.29381450.2387129X-RAY DIFFRACTION99.93
8.18-48.850.2341450.20187231X-RAY DIFFRACTION99.41
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)
11.86274479390.0313078089138-0.3900778602611.1184561142-0.3167356847881.44089216979-0.0394528156072-0.2737975936230.396013379920.166753840249-0.07394513863810.00610226388825-0.0143451708235-0.0562753971594-0.0003980691234340.693177591726-0.02420451994270.1115257836720.8881144500760.1071102858150.641094454217-27.0710813697103.3366941161.9318054248
22.484020267910.8041611507230.2245577385492.57716414192-0.1877197800471.933196022430.0261927631269-0.3237968115610.118416813562-0.1251473899530.0102119546360.515717270653-0.293777771305-0.0458570999753-0.06004276386580.8499061737220.05128236471210.1351061935170.922313385969-0.1325714888380.90701625046-42.8284922728133.29555698548.0598041539
32.020319822920.29571790409-0.2405986187581.95377479642-0.2371694277692.037863773890.03590625009320.3874777651680.151251716441-0.0927304635237-0.00468927047372-0.365310194745-0.156969375377-0.00913774310059-0.01962318469360.898690458682-0.000558155841489-0.05190967065060.660024220904-0.002542026216270.828776841378-29.7207165456125.13318229614.6710155572
43.01962484991-0.6065011710650.6617905550911.9530972837-0.4303827478361.275533572960.16906172923-0.144593547566-0.263050297253-0.118037936583-0.00137794150346-0.1645883836-0.03996140311470.15977495448-0.1233183090880.893408049026-0.04977661698880.09520128455970.6712443962150.01905209629140.907465642807-11.157442654597.339524877129.3933259647
52.767970711031.14749502717-0.1385821562061.673520413420.1839776901982.07970743223-0.0646486205520.2432508828110.195422342119-0.0508137142774-0.1588018931-0.002886147576630.04674011905720.1735941341070.1846168522820.787459338820.00836663255289-0.009896092658820.7173658304910.0649439034690.89236711774613.991703102124.00959884428.0079864467
62.40164574523-0.5592959834880.2068345899871.8285974724-0.4481927312011.64128941742-0.183608683186-0.162792758880.9615640225150.0930656032137-0.0131995726788-0.130383746441-0.0354536473554-0.1861672307760.1701533883580.994774286478-0.0397043928737-0.1492615341750.711545482417-0.07613167110121.31914134003-9.6508939355151.90346881929.3662032117
72.094062328130.6489651552460.2928268790811.03821731297-0.21629395231.855605755830.129392118567-0.215064104098-0.382949116183-0.0200287539407-0.04408120184730.179682907889-0.170468126806-0.161802146177-0.1061771161830.928929556339-0.06614643508290.03622623904990.916952829767-0.3344260672920.905778522104-13.4773703109146.54827536465.4179372457
82.547936390280.491661185169-0.933650447382.27211207028-0.9335800827111.150270827410.0875056773979-0.670521371976-0.4468374177320.30502147342-0.19535282396-0.5013948485280.06028552837860.239992183970.1306350507650.915737491951-0.142253693725-0.1016801451991.116658768890.1147456058880.9403466922266.97967971432116.16828502663.1145301325
90.8963976498690.224345328412-0.6157348719991.579566592920.03605300521781.48718924967-0.0731073506518-0.4602685300750.09225929908390.301598187270.136259673982-0.315757806068-0.06434307534280.3634485832740.09177318986241.23086645796-0.145339090233-0.1519299456581.743085666650.03367348119391.5393201738437.4677375924126.81249632880.2938880866
100.334419954464-0.1261328571950.575921535092.48662745340.1103016990971.313717098110.095187413965-0.4850085631510.0364433737980.0442867536034-0.515140885562-0.3931871563890.1353090893930.3867347630470.3056560898031.62354847545-0.160021150473-0.1515066707672.213706824280.1333964534931.775137190167.0219842461127.79907405899.9816181426
112.999000628990.5885797775380.05060990264220.702815265593-0.400328143143.00502988585-0.019318245188-0.09097789466860.3713086977860.156304702006-0.335775064263-0.0463768070196-0.201998273840.1941242838810.297835943110.792808266774-0.101400694053-0.08375415021860.8730468090810.2485760518031.106307371747.6460889564137.4405425734.0136205202
123.30375276685-0.3602345931261.198715508750.615564857393-1.361109019164.43602384570.2857481748390.3109422853170.12632144889-0.185755371420.0566611701273-0.3198804559040.002586434718620.421214752054-0.407918737010.934259612581-0.137938975245-0.08028051571321.192965064930.06124968148951.5503686660582.3538130874143.84708520731.6028223589
131.61267610601-0.42757477281-0.06263087140132.706970702510.6908603450320.6168072454010.189861593251-0.0708645852209-0.5547850888830.255736368634-0.0400831526262-0.3951442339740.1664450831170.0327715964948-0.1571009619911.12000076616-0.0374113013682-0.2507467335440.8894697976650.01523175869861.9220840137714.040554064179.94169735429.0646811953
142.18295820187-1.24560225680.002537893504452.46572348128-0.2326403532032.12203743594-0.009520239622370.12428400397-0.26174565104-0.0707418203833-0.00801998620365-1.66562910534-0.3551964440140.5168449554540.03881678819491.16220168493-0.1117553105390.05832697613311.0289054667-0.2049298883772.2850569904830.2835333805210.54290423122.662153721
151.58987022446-0.1903038167570.3920384582752.14635997807-0.4210710303092.27189384751-0.06581400184540.131963727058-0.1374701535870.145018200634-0.125585846639-0.04213196270480.166627257228-0.1308540650290.2267510351630.887864396678-0.0592223770726-0.05607392701030.935303931915-0.253595141750.5779606421229.7864756842174.53815448273.535795879
160.6386770866831.074905061810.3987747995444.043157090950.5700664666833.66699581925-0.322589322967-0.08883639223250.4649410659050.4212513254810.250675831934-0.563264150810.0121400841983-0.0527127601304-0.07184159861811.067229222230.085653467737-0.1607360473281.21385005217-0.2758044912261.4586315611124.0288100087204.12568856886.7832857148
171.070168137020.341479639361-0.0325964565272.22297035551-0.3168551659281.328723475430.0368389923768-0.1208135577240.369516636265-0.410989767838-0.1998785104140.441376858617-0.109167679633-0.3916387418960.1811347636530.9703775433470.118880035476-0.1854434952591.34853310801-0.1971163460481.62149327622-77.2306644146121.16332346547.9674967314
181.65426667152-0.09258851522150.8460423880362.14535489664-0.997040714010.831606728890.06750917664050.152979067763-0.364338052831-0.5451627924880.2916349346261.578617854330.331592294459-1.03872635417-0.2892656742151.74525203291-0.159812901456-0.08367503424072.574505665550.3280121174162.54471485683-111.727722014118.0771134250.6211720823
193.075682328680.824614816150.388401370321.914754586170.5176823544472.73800858085-0.03724097447580.77782272536-0.483532574146-0.1345830693850.255656250640.3377198449420.236966998295-0.318986273225-0.1566168167560.802138621983-0.118157171289-0.110499950961.05048783132-0.005804015340930.98839119429-59.9704569646110.076629480.581483065473
201.539464996820.4416276072251.329716693630.9067137332631.054898565181.68759578488-0.08624366261021.36493237699-0.662527963546-0.3741107223540.191253401220.3427999793710.903587499402-0.238617313606-0.1113013949171.63309593505-0.402288399386-0.1573384786262.73843521096-0.03323542028941.72079883229-85.535509139999.8329733946-22.1763580554
211.665345725040.1572061351460.6450539809582.106358197360.1025696996731.31403255110.1814248235630.011377333397-0.0117718154241-0.107472144410.05282168122040.420485660216-0.0855070953648-0.0400658430549-0.2110083204670.9961425075640.0642247036692-0.1143463367970.84333763473-0.05398738926451.49642611802-30.588730444169.413360808615.529282834
221.1776354468-0.8405290289740.8523723628191.925251787510.1539011465685.85391913904-0.2959353917540.04216221773580.08572961336980.0204345174515-0.4277308106630.1760983802760.0303789066933-0.9925272972950.6705251565251.00451468796-0.0398712341552-0.2812469153191.01733096553-0.2060017069591.76833887128-40.128784551838.95039167020.539815785304
231.98106240130.148746737457-0.5605610061132.329786850890.2636198650412.37758559637-0.1857165183-0.070026449591-0.2677643357080.0426387048565-0.1138306633290.187149363-0.0944251973306-0.1035161215770.18903398010.770225925364-0.09954371302440.03364195560591.106271357050.2804471130221.10843242566-52.561582649977.029748316158.4782307526
241.73496819132-0.780617616532-1.260767810582.18079618325-0.2583569404761.22949117181-0.1403378640640.144109373824-0.8420689863280.607168078422-0.00361092431660.2666712435870.678942790532-0.63060699130.1509478776311.25952872465-0.3809928198420.1168001965471.43702782390.2106500798741.28692648102-74.743724683350.311117006965.6210238859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain R
2X-RAY DIFFRACTION2chain U
3X-RAY DIFFRACTION3chain X
4X-RAY DIFFRACTION4chain A
5X-RAY DIFFRACTION5chain L
6X-RAY DIFFRACTION6chain D
7X-RAY DIFFRACTION7chain I
8X-RAY DIFFRACTION8chain O
9X-RAY DIFFRACTION9(resid 1:109 and chain N) or (resid 1:122 and chain M)
10X-RAY DIFFRACTION10(resid 110:218 and chain N) or (resid 123:224 and chain M)
11X-RAY DIFFRACTION11(resid 1:109 and chain K) or (resid 1:122 and chain J)
12X-RAY DIFFRACTION12(resid 110:218 and chain K) or (resid 123:224 and chain J)
13X-RAY DIFFRACTION13(resid 1:109 and chain C) or (resid 1:122 and chain B)
14X-RAY DIFFRACTION14(resid 110:218 and chain C) or (resid 123:224 and chain B)
15X-RAY DIFFRACTION15(resid 1:109 and chain H) or (resid 1:122 and chain G)
16X-RAY DIFFRACTION16(resid 110:218 and chain H) or (resid 123:224 and chain G)
17X-RAY DIFFRACTION17(resid 1:109 and chain T) or (resid 1:122 and chain S)
18X-RAY DIFFRACTION18(resid 110:218 and chain T) or (resid 123:224 and chain S)
19X-RAY DIFFRACTION19(resid 1:109 and chain W) or (resid 1:122 and chain V)
20X-RAY DIFFRACTION20(resid 110:218 and chain W) or (resid 123:224 and chain V)
21X-RAY DIFFRACTION21(resid 1:109 and chain F) or (resid 1:122 and chain E)
22X-RAY DIFFRACTION22(resid 110:218 and chain F) or (resid 123:224 and chain E)
23X-RAY DIFFRACTION23(resid 1:109 and chain Q) or (resid 1:122 and chain P)
24X-RAY DIFFRACTION24(resid 110:218 and chain Q) or (resid 123:224 and chain P)

+
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