PDB-9eu2: GH29A alpha-L-fucosidase

ID or keywords:

Entry

Database: PDB / ID: 9eu2

Title

GH29A alpha-L-fucosidase

Components

Alpha-L-fucosidase

Keywords

HYDROLASE / GH29A / GH29 / fucosidase

Function / homology

Function and homology information

alpha-L-fucosidase / alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome / metal ion binding
Similarity search - Function

Biological species

Tannerella forsythia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.84 Å

Authors

Yang, Y.Y. / Zeuner, B. / Morth, J.P.

Funding support

Denmark, 2items

Citation

Journal: Febs J. / Year: 2025
Title: Structural elucidation and characterization of GH29A alpha-l-fucosidases and the effect of pH on their transglycosylation.
Authors: Yang, Y. / Holck, J. / Thorhallsson, A.T. / Hunt, C.J. / Yang, H. / Morth, J.P. / Meyer, A.S. / Zeuner, B.

History

Deposition	Mar 27, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9eu2.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb9eu2.ent.gz	841.9 KB	Display	PDB format
PDBx/mmJSON format	9eu2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9eu2_validation.pdf.gz	463.2 KB	Display	wwPDB validaton report
Full document	9eu2_full_validation.pdf.gz	469.2 KB	Display
Data in XML	9eu2_validation.xml.gz	89.5 KB	Display
Data in CIF	9eu2_validation.cif.gz	125 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eu/9eu2 ftp://data.pdbj.org/pub/pdb/validation_reports/eu/9eu2	HTTPS FTP

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Related structure data

Related structure data	9eu1C 9eu3C 9eu4C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Alpha-L-fucosidase

B: Alpha-L-fucosidase

C: Alpha-L-fucosidase

D: Alpha-L-fucosidase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	147.912, 147.912, 197.086
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21
Space group name Hall	P3₂2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3 #4: x-y,-y,-z+1/3 #5: -x,-x+y,-z+2/3 #6: y,x,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-501- ZN

#1: Protein	Alpha-L-fucosidase Mass: 49849.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: BFO_2737 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8UMQ6, alpha-L-fucosidase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1806 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.12 Å³/Da / Density % sol: 60.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 20% Ethylene glycol 0.1M HEPES pH 7.3 10% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: 293 / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 4, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8731 Å / Relative weight: 1
Reflection	Resolution: 1.84→47.02 Å / Num. obs: 215060 / % possible obs: 99.92 % / Redundancy: 20.7 % / B_iso Wilson estimate: 31.79 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.1315 / R_pim(I) all: 0.02981 / R_rim(I) all: 0.1349 / Net I/σ(I): 18
Reflection shell	Resolution: 1.84→1.906 Å / Redundancy: 20.7 % / R_merge(I) obs: 1 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 21308 / CC_1/2: 0.717 / CC star: 0.914 / R_pim(I) all: 0.5029 / R_rim(I) all: 1 / % possible all: 99.98

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
autoPROC		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.84→47.02 Å / SU ML: 0.2261 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.0396
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.188	3908	0.93 %
R_work	0.1623	414262	-
obs	0.1625	215060	99.92 %

Solvent computation

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

Displacement parameters

B_iso mean: 35.69 Å²

Refinement step

Cycle: LAST / Resolution: 1.84→47.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13614	0	48	1806	15468

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	14075
X-RAY DIFFRACTION	f_angle_d	0.9517	19083
X-RAY DIFFRACTION	f_chiral_restr	0.0526	1997
X-RAY DIFFRACTION	f_plane_restr	0.0129	2461
X-RAY DIFFRACTION	f_dihedral_angle_d	6.442	1880

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 (%)
1.84-1.86	0.4512	131	0.3387	14808	X-RAY DIFFRACTION	99.91
1.86-1.89	0.3404	138	0.3137	14715	X-RAY DIFFRACTION	99.95
1.89-1.91	0.2922	142	0.293	14893	X-RAY DIFFRACTION	99.97
1.91-1.94	0.2657	140	0.2688	14727	X-RAY DIFFRACTION	99.95
1.94-1.96	0.2635	144	0.2529	14875	X-RAY DIFFRACTION	99.99
1.96-1.99	0.2703	140	0.2355	14779	X-RAY DIFFRACTION	99.97
1.99-2.03	0.2137	136	0.219	14827	X-RAY DIFFRACTION	99.97
2.03-2.06	0.241	138	0.2094	14806	X-RAY DIFFRACTION	99.96
2.06-2.09	0.231	142	0.202	14730	X-RAY DIFFRACTION	100
2.09-2.13	0.2209	134	0.1918	14778	X-RAY DIFFRACTION	99.99
2.13-2.17	0.2096	144	0.1832	14874	X-RAY DIFFRACTION	99.97
2.17-2.22	0.2313	142	0.1753	14797	X-RAY DIFFRACTION	99.98
2.22-2.27	0.1993	140	0.1816	14808	X-RAY DIFFRACTION	99.96
2.27-2.32	0.1921	138	0.1651	14813	X-RAY DIFFRACTION	99.99
2.32-2.38	0.1972	138	0.1525	14771	X-RAY DIFFRACTION	99.99
2.38-2.44	0.1849	140	0.1462	14817	X-RAY DIFFRACTION	99.97
2.44-2.51	0.187	144	0.1578	14824	X-RAY DIFFRACTION	99.96
2.51-2.59	0.1878	140	0.1557	14859	X-RAY DIFFRACTION	100
2.59-2.69	0.1945	142	0.1515	14727	X-RAY DIFFRACTION	99.99
2.69-2.79	0.1806	134	0.1432	14827	X-RAY DIFFRACTION	99.93
2.79-2.92	0.1763	142	0.1712	14759	X-RAY DIFFRACTION	99.96
2.92-3.07	0.1864	150	0.1615	14811	X-RAY DIFFRACTION	99.99
3.07-3.27	0.2086	134	0.1559	14820	X-RAY DIFFRACTION	99.98
3.27-3.52	0.185	142	0.1533	14795	X-RAY DIFFRACTION	100
3.52-3.87	0.1693	134	0.1491	14808	X-RAY DIFFRACTION	99.98
3.87-4.43	0.1432	144	0.1285	14796	X-RAY DIFFRACTION	99.99
4.43-5.58	0.1595	142	0.1213	14805	X-RAY DIFFRACTION	100
5.58-47.02	0.1694	133	0.1664	14613	X-RAY DIFFRACTION	98.57

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	0.714823836427	-0.166673759815	-0.130470604111	1.90429492004	0.370495968818	0.909151671069	-0.00662688813442	0.0555265353918	-0.0235704521654	0.0343032218387	-0.109672899358	0.387873803978	0.0295314736608	-0.203404106098	-0.00119427410648	0.243887869492	0.017815248388	-0.00212228933975	0.296701577925	-0.059977784046	0.301738684303	33.7562790815	3.88777393732	13.5526986289
2	0.0464084178629	0.0625714042155	-0.0399780394527	0.0987725715949	-0.0466111345838	0.0849923187645	0.0750549282876	0.15530857059	0.227864359088	-0.333376135061	-0.117879119996	0.225643358918	-0.261307001157	-0.238498660423	-0.000143657348747	0.386099201826	0.1100878709	-0.0910690552948	0.367468003733	-0.0377032520577	0.382820417139	35.2301561789	20.9283352256	4.69510018713
3	0.108223043601	0.260637544608	-0.0734828663159	0.695514470753	-0.206261845283	0.350204935181	0.0109654274326	-0.025466202633	0.0628264662342	-0.034787522453	-0.0116411752776	0.00508436224931	-0.058518886396	-0.0508718644954	-1.14606234087E-5	0.310877246785	0.0556635905145	-0.0374311961691	0.253161108552	-0.0381185932554	0.280726278764	48.8750242385	21.5242729071	12.17042379
4	0.132236642414	0.176486629594	0.053352242831	0.2615943225	-0.0762313346945	0.300643878988	0.0101804241744	0.111384064442	0.171916539439	-0.223431598529	-0.0392652718789	-0.162096828824	-0.190045742617	0.160843426412	-0.000145326520248	0.424931976936	0.0837742317003	-0.0438014260102	0.308891271333	-0.0467168131136	0.421815490409	50.5225700288	43.7966691994	12.5597029978
5	0.127048714248	-0.0904026634473	0.018590821973	0.539041199573	-0.0140291224029	0.536547560079	0.00198426329565	0.0800089726746	0.134747287812	-0.10821418625	-0.0284107262052	0.0746187252825	-0.0943624167367	-0.064459365189	4.44366703633E-5	0.427330044285	0.0770038853572	-0.0269552867167	0.319627905396	-0.0367573565604	0.406990114775	47.5597286872	43.8233365955	12.0226674241
6	0.28381659494	-0.266824669581	-0.287879613301	0.486094539866	0.0864300336465	0.429245127076	0.0219514045795	0.0435247797832	0.0495807503004	-0.128632134129	-0.05649095544	0.40853940151	-0.0995274561394	-0.0836408486255	6.72733143533E-5	0.331763154	0.00331854782579	-0.0575448210694	0.325887122886	-0.026130021929	0.428041721826	37.4663721773	-8.96023453098	-42.8240685805
7	0.216017160756	0.167731315506	0.0862593163309	0.25784769182	-0.127843022217	0.296007374195	-0.0312021855418	0.0277488298069	0.186700932712	-0.4120955079	0.0465483796821	0.141967531197	-0.189974286083	0.0214853249566	2.72329848189E-5	0.405675512614	0.00061730546681	-0.0503666790302	0.306470496479	-0.000702008220241	0.341146855446	46.5225834381	2.74468689005	-47.2026855861
8	0.895441064172	0.396482761448	0.135989537442	1.87665836791	0.274022096778	0.660300895262	-0.00765711950138	0.00893500653235	0.137294119105	-0.159438799502	-0.135820985611	0.719186796476	-0.115926829966	-0.243798589776	-0.000352169710383	0.327400080524	0.0310240369899	-0.0918511484444	0.35251329504	-0.055658471338	0.541211280908	30.3029634551	-3.81887390807	-43.3002196455
9	0.0663034654333	-0.0283955306052	-0.00400419067529	0.0857108019973	-0.0670317539548	0.106218056074	0.0952338442687	-0.139932056688	-0.0543646536025	0.379106291369	-0.127565761289	0.482401663615	0.223035039503	-0.103409494207	-0.000115996951242	0.390203104437	-0.0546011251612	0.0496533923991	0.368154278217	-0.052414925016	0.443183784797	35.0681475167	-21.1425272132	-34.9201069976
10	0.0316964930434	-0.0455432477621	0.0553614136309	0.550426306291	0.145947489651	0.305259940128	-0.00803842587229	0.0769170313974	0.0509121889655	-0.01944870494	0.00760326475636	-0.0301345563894	-0.0882844423733	0.0590543858382	-5.55400281802E-6	0.318078587958	-0.0251096805318	-0.00421077047194	0.286370782138	-0.0234366590797	0.302065562572	51.0160391723	-15.9066440788	-42.4579238262
11	0.156063849647	-0.102506202149	-0.0118941304563	0.146656505741	0.0342046644882	0.0213413366627	-0.0729670304023	0.0985166208319	-0.147242203894	-0.119172985413	0.0356801230064	0.213755673706	0.0426600147054	-0.0765989463412	1.08962491131E-5	0.302947614785	-0.028299228548	-0.0154498999562	0.294428036598	-0.0654688280094	0.31805404934	42.8897542842	-35.6381017367	-43.3472529714
12	0.19461632888	-0.236926201793	-0.108613145214	0.317915328314	0.00703208114779	0.31640183108	-0.0905214690187	0.00945340962013	-0.00235134490529	0.0280978834837	0.00426106281088	-0.020448800619	0.0796353681348	0.0788217321315	-1.77565837847E-5	0.334083700958	-0.0394731278288	0.0323695895051	0.296941950424	-0.0666790100727	0.326914320002	50.4481874723	-43.8584729434	-43.3347688845
13	0.126381857943	-0.0202902796788	-0.0429958313065	0.576438541489	0.000636592437666	0.459652412236	-0.0788607497878	-0.0360576304264	-0.104016095192	0.00588860569383	0.0118797372483	0.0415357353176	0.0962108077509	-0.0496568866682	8.27409248831E-5	0.312528969625	-0.0384160352901	0.0246358869723	0.315886980518	-0.0570306202951	0.324826356438	48.0917070954	-44.0792080377	-42.8073568989
14	0.215022567742	-0.0611246360804	0.158058319385	0.180098933469	0.0786412304201	0.226520917316	0.0788803491576	0.305181804787	-0.0200009717445	-0.142384343854	0.10133696027	-0.514022485539	0.372349353369	0.185441358104	-9.86599331982E-5	0.406651238382	0.0920640954775	0.00617492801213	0.387814972905	-0.0556682365004	0.450096000432	74.9243807898	-39.0317482458	-4.71698252288
15	0.355158436493	-0.0146539598649	0.0963001347089	0.924217786535	0.43008938181	0.743109594563	-0.0222721229834	0.0336600522117	-0.00582556514481	0.0346478490411	-0.00445893972143	-0.0500624502642	0.0311614576288	0.0319760893	-9.72780237796E-8	0.265554568666	0.0171837789252	-0.00329394447657	0.223927969139	-0.00268650795261	0.19533104752	62.9660251804	-23.7398313233	-1.26864356728
16	0.38133426223	0.136176055844	-0.0260332166489	0.795415038489	0.0627591120873	0.886167729616	-0.0455847070448	0.0025842815198	-0.0694851680761	-0.00386157845831	-0.0128366163564	0.169975862554	0.171195206542	-0.152923616093	-1.22421918877E-5	0.338740281424	-0.0281841780801	0.0102716212042	0.289953667697	-0.0391808591915	0.306567293444	50.9578136229	-51.5525041692	-22.2389835881
17	0.448319920328	-0.533576420136	-0.170912334413	0.855810068421	-0.0313974873098	0.463319981024	0.0384786945409	0.0547181216041	0.0192203917163	-0.0837863062392	0.0220843944083	0.0231157946486	-0.125425229944	-0.0184856707012	8.52401017269E-6	0.403789196971	-0.0153770981193	0.0142122217759	0.26904916342	0.0144947614198	0.28272564098	62.9746432603	23.5894774887	-29.9871527065
18	0.205031572696	0.208438421789	-0.0194970554035	0.219039089031	0.0713978809005	0.288372361319	-0.0131840786451	0.0856168991266	-0.0201175177237	-0.240080532819	-0.0291392569017	0.097545049419	-0.0802824799452	-0.0983246191776	-3.75405565607E-5	0.397182578693	8.89610714058E-5	-0.0164459571555	0.258006984929	0.0200457310342	0.281478956099	54.9504650616	17.9515198407	-41.2237827076
19	0.63385812117	0.377652095996	0.0470229392171	0.492875179803	0.235537587811	0.820654373442	0.0166843292513	0.119185387711	0.0468720851221	-0.248388274412	-0.0209290091325	-0.115516312908	-0.135733900248	0.060401653413	-1.5925566755E-5	0.404367342683	-0.0290178288107	0.023537395748	0.274625913387	0.0304090884908	0.298850699277	65.0481860651	20.2089468591	-39.2417744029
20	0.675791866853	0.386211918458	-0.0170100957671	0.776056718433	0.301602802327	0.927002740312	0.0518039206799	-0.102441885233	-0.0523773698342	0.0705796705007	0.0485306661562	-0.262108975136	-0.0282813061382	0.178048673468	5.13058427361E-5	0.350456113377	-0.0319050617574	0.0126301440212	0.307061613843	0.0137361049902	0.351664288849	74.4992584133	19.9251641964	-28.2205849514
21	0.115192984097	-0.0805721277565	-0.0856339436382	0.110488571426	-0.00223205025798	0.110242316209	0.0236321499774	-0.247880015459	-0.0129038841158	0.324581668644	-0.00726504731124	-0.118018362841	-0.0968182089984	0.0249270199364	8.97731941162E-5	0.456891186039	-0.0253734413449	0.00110032383242	0.350609178664	0.00668705686618	0.339262989968	64.600557235	28.2550460734	-15.7165150076
22	0.232389784276	-0.364371527495	-0.0712912771274	0.428816034466	0.0762627573923	0.518451701588	-0.0156373315961	0.039270745177	0.049614016097	-0.0688079472765	-0.0118095257163	0.174010075051	-0.154703949455	-0.135576031982	-9.35113715113E-5	0.414882241093	0.025290515981	0.00786984795683	0.270469483431	0.000468717031762	0.359685120437	51.7386171245	33.8516888236	-22.6527961188
23	0.131298703475	-0.156242588134	-0.030475591877	0.171184670139	0.0621203013926	0.269034831563	-0.0691643321918	-0.00827048510444	0.117905448425	0.116917905746	0.0753069309326	0.109350124869	-0.369759254764	-0.205095767622	-0.000124494149535	0.626102779125	0.0888866414034	-0.00749446809671	0.285640273017	-0.0144162253402	0.407487942264	49.8304910462	51.2311724423	-9.16473575117
24	0.100493671651	0.0842726744718	0.125271378909	0.35503227702	-0.0564445896189	0.580377645872	-0.0978657968533	0.00872108998023	0.113335770824	-0.0177632326375	0.126153288201	0.0315725062656	-0.480585677793	-0.0781556025975	-5.51058436502E-5	0.670943543903	0.0773514041566	-0.011752726279	0.356981446465	-0.0180601615377	0.469488514604	52.1031113757	51.3818136175	-8.09642377715

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 25 through 266 )	A	A	25 - 266	1 - 242
2	2	chain 'A' and (resid 267 through 287 )	A	A	267 - 287	243 - 263
3	3	chain 'A' and (resid 288 through 382 )	A	A	288 - 382	264 - 358
4	4	chain 'A' and (resid 383 through 412 )	A	A	383 - 412	359 - 388
5	5	chain 'A' and (resid 413 through 446 )	A	A	413 - 446	389 - 422
6	6	chain 'B' and (resid 26 through 69 )	B	B	26 - 69	1 - 44
7	7	chain 'B' and (resid 70 through 97 )	B	B	70 - 97	45 - 72
8	8	chain 'B' and (resid 98 through 266 )	B	B	98 - 266	73 - 241
9	9	chain 'B' and (resid 267 through 287 )	B	B	267 - 287	242 - 262
10	10	chain 'B' and (resid 288 through 354 )	B	B	288 - 354	263 - 329
11	11	chain 'B' and (resid 355 through 382 )	B	B	355 - 382	330 - 357
12	12	chain 'B' and (resid 383 through 412 )	B	B	383 - 412	358 - 387
13	13	chain 'B' and (resid 413 through 445 )	B	B	413 - 445	388 - 420
14	14	chain 'C' and (resid 21 through 42 )	C	C	21 - 42	1 - 22
15	15	chain 'C' and (resid 43 through 382 )	C	C	43 - 382	23 - 362
16	16	chain 'C' and (resid 383 through 445 )	C	C	383 - 445	363 - 425
17	17	chain 'D' and (resid 26 through 69 )	D	D	26 - 69	1 - 44
18	18	chain 'D' and (resid 70 through 97 )	D	D	70 - 97	45 - 72
19	19	chain 'D' and (resid 98 through 164 )	D	D	98 - 164	73 - 139
20	20	chain 'D' and (resid 165 through 266 )	D	D	165 - 266	140 - 241
21	21	chain 'D' and (resid 267 through 287 )	D	D	267 - 287	242 - 262
22	22	chain 'D' and (resid 288 through 382 )	D	D	288 - 382	263 - 357
23	23	chain 'D' and (resid 383 through 411 )	D	D	383 - 411	358 - 386
24	24	chain 'D' and (resid 412 through 446 )	D	D	412 - 446	387 - 421

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