PDB-9emr: Crystal Structure of DC-SIGN in complex with AL90

ID or keywords:

Entry

Database: PDB / ID: 9emr

Title

Crystal Structure of DC-SIGN in complex with AL90

Components

DC-SIGN, CRD domain

Keywords

SUGAR BINDING PROTEIN / DC-SIGN / glycomimetic

Function / homology

Function and homology information

B cell adhesion / cell-cell recognition / intracellular transport of virus / peptide antigen transport / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / pattern recognition receptor activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Jakob, R.P. / Cramer, J. / Maier, T.

Funding support

Germany, 1items

Citation

Journal: J.Med.Chem. / Year: 2024
Title: Thermodynamics-Guided Design Reveals a Cooperative Hydrogen Bond in DC-SIGN-targeted Glycomimetics.
Authors: Nemli, D.D. / Jiang, X. / Jakob, R.P. / Gloder, L.M. / Schwardt, O. / Rabbani, S. / Maier, T. / Ernst, B. / Cramer, J.

History

Deposition	Mar 9, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 13, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9emr.cif.gz	254.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9emr.ent.gz		Display	PDB format
PDBx/mmJSON format	9emr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/em/9emr ftp://data.pdbj.org/pub/pdb/validation_reports/em/9emr	HTTPS FTP

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Related structure data

Related structure data	9emqC 9emsC 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
Related items in Molecule of the Month	#232 - Apr 2019 Proteins and Biominerals similarity (8) #75 - Mar 2006 Tissue Factor similarity (8) #134 - Feb 2011 Integrin similarity (6) #148 - Apr 2012 Ras Protein similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #69 - Sep 2005 Cholera Toxin similarity (1) #222 - Jun 2018 Proteins and Nanoparticles similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#232 - Apr 2019
Proteins and Biominerals
similarity (8)
#75 - Mar 2006
Tissue Factor
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#134 - Feb 2011
Integrin
similarity (6)
#148 - Apr 2012
Ras Protein
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#195 - Mar 2016
RAF Protein Kinases
similarity (1)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#69 - Sep 2005
Cholera Toxin
similarity (1)
#222 - Jun 2018
Proteins and Nanoparticles
similarity (1)

Deposited unit

A: DC-SIGN, CRD domain

B: DC-SIGN, CRD domain

C: DC-SIGN, CRD domain

hetero molecules

56 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DC-SIGN, CRD domain

hetero molecules

defined by author
Evidence: gel filtration
18.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DC-SIGN, CRD domain

hetero molecules

defined by author
18.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: DC-SIGN, CRD domain

hetero molecules

defined by author
18.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.861, 59.866, 75.227
Angle α, β, γ (deg.)	90.000, 91.390, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 253 through 281 or resid 283 through 306 or resid 308 through 501))
2	1	(chain B and (resid 253 through 281 or resid 283 through 306 or resid 308 through 501))
3	1	(chain C and (resid 253 through 281 or resid 283 through 306 or resid 308 through 501))

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	CYS	CYS	ILE	ILE	(chain A and (resid 253 through 281 or resid 283 through 306 or resid 308 through 501))	A	A	253 - 281	8 - 36
1	2	ALA	ALA	GLN	GLN	(chain A and (resid 253 through 281 or resid 283 through 306 or resid 308 through 501))	A	A	283 - 306	38 - 61
1	3	SER	SER	A1H5Y	A1H5Y	(chain A and (resid 253 through 281 or resid 283 through 306 or resid 308 through 501))	A	A - G	308 - 504	63
2	1	CYS	CYS	ILE	ILE	(chain B and (resid 253 through 281 or resid 283 through 306 or resid 308 through 501))	B	B	253 - 281	8 - 36
2	2	ALA	ALA	GLN	GLN	(chain B and (resid 253 through 281 or resid 283 through 306 or resid 308 through 501))	B	B	283 - 306	38 - 61
2	3	SER	SER	A1H5Y	A1H5Y	(chain B and (resid 253 through 281 or resid 283 through 306 or resid 308 through 501))	B	B - K	308 - 504	63
3	1	CYS	CYS	ILE	ILE	(chain C and (resid 253 through 281 or resid 283 through 306 or resid 308 through 501))	C	C	253 - 281	8 - 36
3	2	ALA	ALA	GLN	GLN	(chain C and (resid 253 through 281 or resid 283 through 306 or resid 308 through 501))	C	C	283 - 306	38 - 61
3	3	SER	SER	A1H5Y	A1H5Y	(chain C and (resid 253 through 281 or resid 283 through 306 or resid 308 through 501))	C	C - O	308 - 504	63

#1: Protein	DC-SIGN, CRD domain / C-type lectin domain family 4 member L / Dendritic cell-specific ICAM-3-grabbing non-integrin 1 / ...C-type lectin domain family 4 member L / Dendritic cell-specific ICAM-3-grabbing non-integrin 1 / DC-SIGN / DC-SIGN1 / CD209 antigen Mass: 18160.051 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD209, CLEC4L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NNX6
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-A1H5Y / (2~{R},3~{S},4~{R},5~{S},6~{S})-6-[(2~{S})-2,3-bis(oxidanyl)propoxy]-2-(hydroxymethyl)-5-(4-phenyl-1,2,3-triazol-1-yl)oxane-3,4-diol Mass: 381.380 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₇H₂₃N₃O₇ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.68 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Succinic acid pH 7.0, 15% w/v Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 9, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 1.9→51.915 Å / Num. obs: 36026 / % possible obs: 98.3 % / Redundancy: 12.7 % / CC_1/2: 0.986 / R_pim(I) all: 0.08 / Net I/σ(I): 7.2
Reflection shell	Resolution: 1.9→1.94 Å / Redundancy: 8.7 % / Num. unique obs: 2045 / CC_1/2: 0.529 / R_pim(I) all: 0.821 / % possible all: 86.3

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→51.915 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1936	1722	4.79 %
R_work	0.159	34248	-
obs	0.1606	35970	98.32 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 127.54 Å² / B_iso mean: 27.9847 Å² / B_iso min: 11.39 Å²

Refinement step

Cycle: final / Resolution: 1.9→51.915 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3210	0	159	411	3780
B_iso mean	-	-	30.1	36.89	-
Num. residues	-	-	-	-	396

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	2030	X-RAY DIFFRACTION	6.602	TORSIONAL
1	2	B	2030	X-RAY DIFFRACTION	6.602	TORSIONAL
1	3	C	2030	X-RAY DIFFRACTION	6.602	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.9-1.9559	0.2921	127	0.2526	2506	87
1.9559-2.019	0.246	137	0.2079	2810	97
2.019-2.0912	0.2277	125	0.1846	2892	100
2.0912-2.1749	0.2364	153	0.1789	2863	100
2.1749-2.2739	0.2104	136	0.1716	2894	100
2.2739-2.3938	0.1801	155	0.1574	2893	100
2.3938-2.5438	0.1674	148	0.1624	2824	99
2.5438-2.7402	0.1884	134	0.1513	2911	100
2.7402-3.0159	0.1859	163	0.1504	2886	100
3.0159-3.4523	0.1963	150	0.1498	2893	100
3.4523-4.3491	0.1766	118	0.1304	2928	99
4.3491-51.915	0.1789	176	0.1589	2948	99

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	0.0512	-0.0785	-0.0443	0.1178	0.0675	0.0376	-0.0484	0.2395	0.0451	-0.1604	-0.134	0.2938	-0.4351	-0.0741	-0.0092	0.2004	0.0313	-0.0125	0.2386	0.0199	0.1896	-31.9496	18.6449	-1.1343
2	0.1576	-0.1213	0.0772	0.1098	-0.0091	0.1835	-0.1049	0.1756	0.0609	-0.1163	0.0082	0.024	0.0172	0.0999	-0.1389	0.1117	0.0036	0.0133	0.1814	0.0078	0.179	-25.7729	17.5992	8.556
3	0.2202	0.1808	-0.1148	0.3306	-0.0324	0.1498	-0.1288	0.1459	0.2146	-0.0829	0.1783	0.4032	-0.0287	-0.0929	0.0134	0.1739	-0.0023	0.0198	0.1374	-0.0055	0.1945	-27.7327	23.6451	15.6956
4	0.0527	-0.0013	0.0473	0.0375	-0.0164	0.0603	0.0513	0.1761	-0.0738	0.0366	0.0454	0.0286	0.2256	0.0698	0.0001	0.1707	0.0053	0.0012	0.1824	-0.0039	0.1559	-23.6662	7.7677	12.7008
5	0.037	-0.0475	0.0241	0.0579	-0.0293	0.0147	-0.0426	0.1153	-0.0186	0.0608	-0.0928	-0.0466	0.088	0.1035	-0.0013	0.1918	0.022	0.0337	0.1906	-0.0053	0.1544	-19.5035	17.2734	18.7741
6	0.0317	0.015	0.0202	0.0157	-0.004	0.0214	-0.1936	-0.338	0.0741	0.5361	-0.0709	0.1713	-0.0713	-0.1792	-0.0447	0.3226	0.0137	0.0478	0.2175	-0.0314	0.1947	-27.0612	20.3603	30.0078
7	0.0757	0.1265	0.193	0.2065	0.3216	0.5012	0.1005	-0.0645	-0.0148	0.304	-0.0462	0.2649	0.2814	0.0074	0.0949	0.2276	-0.0239	0.0668	0.1913	-0.0067	0.1648	-30.3021	10.6647	26.2092
8	0.0457	0.0328	-0.0553	0.1053	0.013	0.1271	0.0444	-0.1646	0.0315	0.287	-0.0997	0.0328	-0.0385	0.0674	-0.0314	0.2417	-0.0056	-0.0031	0.1924	-0.0183	0.1497	-17.16	13.7574	26.17
9	0.0234	-0.0054	0.0177	0.0301	0.0113	0.0164	0.0916	-0.0494	0.0836	0.1833	0.0109	-0.2116	-0.0066	0.1046	0.0002	0.1806	0.0155	-0.0217	0.2027	-0.0024	0.2409	-15.8009	22.864	18.1456
10	0.2397	0.024	0.266	0.4033	-0.3852	0.7328	-0.0905	0.0719	0.0312	0.1548	-0.0384	0.1774	-0.0611	-0.1495	-0.0629	0.1084	0.0234	0.0208	0.2136	-0.0004	0.2629	-34.9521	18.0235	6.7551
11	0.0345	0.0269	-0.0215	0.0554	-0.0472	0.0346	0.0368	-0.062	-0.1439	-0.2237	-0.0835	-0.0974	0.2692	-0.1676	-0.0029	0.1883	-0.0112	-0.0082	0.1926	-0.0253	0.1508	-25.4355	-20.6709	-1.2269
12	0.0232	0.0425	0.0353	0.1637	0.1622	0.1575	0.0058	0.0527	0.1606	-0.147	-0.0414	0.0373	-0.1055	-0.0165	-0.0101	0.1352	0.0034	0.0177	0.1446	-0.0027	0.1729	-27.4781	-14.8094	8.4952
13	0.0738	0.0736	-0.0431	0.1676	-0.0021	0.037	-0.0121	0.1185	-0.236	0.0972	-0.0037	0.0705	0.0428	-0.0102	-0.0002	0.1156	-0.0184	0.0295	0.1646	-0.0174	0.1686	-31.9984	-19.6038	15.5771
14	0.0959	0.0273	-0.0803	0.0646	-0.034	0.068	0.0902	0.0251	0.0151	-0.1477	-0.0708	-0.2181	-0.01	0.1922	-0.0021	0.1978	-0.0061	-0.0048	0.1343	-0.0135	0.1481	-20.0825	-8.1395	12.6291
15	0.0062	0.0067	0.0047	0.051	0.0497	0.0482	0.0271	0.1275	-0.0333	0.0796	-0.1564	0.1264	-0.1351	0.1236	-0.0025	0.2234	-0.022	0.0205	0.1615	0.014	0.1752	-30.3449	-9.2954	18.7046
16	0.0658	0.0539	-0.0627	0.1059	-0.046	0.0634	-0.1567	-0.2148	-0.1311	0.5228	-0.0768	-0.0022	0.1674	0.213	-0.0139	0.3665	-0.0438	0.0639	0.1952	0.0268	0.1475	-29.1646	-17.4981	29.8915
17	0.0573	-0.0493	-0.0082	0.0417	0.0115	0.0022	-0.1122	-0.0491	-0.1392	0.0765	0.2066	-0.1847	0.0884	0.1192	-0.0007	0.248	0.0125	-0.0169	0.202	0.0259	0.1753	-19.0674	-15.4408	26.1626
18	0.1552	-0.2452	0.0205	0.4273	0.1127	0.2921	-0.1259	-0.0587	-0.0617	0.2889	-0.023	0.1552	-0.0882	-0.0661	-0.077	0.2273	-0.006	0.0337	0.1691	-0.0082	0.1511	-30.6632	-6.4401	24.0729
19	0.2097	0.1343	0.2093	0.1399	0.2577	0.5431	0.0907	-0.0724	-0.154	-0.0523	-0.21	0.0176	0.2118	0.0172	-0.0145	0.2008	0.0356	0.0226	0.1307	0.0027	0.2457	-23.3498	-22.9857	6.6403
20	0.007	0.0059	0.0164	0.0035	0.0091	0.0299	-0.1812	0.1444	0.0854	-0.0751	-0.0071	-0.1016	0.0924	0.2075	-0.0003	0.1579	-0.0066	0.0136	0.2336	-0.0261	0.26	5.415	4.608	-1.1866
21	0.3727	0.0507	-0.1265	0.2805	-0.0914	0.2232	-0.1006	-0.0276	-0.1112	-0.1363	-0.0988	-0.2962	0.0515	-0.0637	-0.3462	0.1258	-0.0015	-0.0035	0.1767	0.0134	0.2466	1.4582	-0.1685	8.5192
22	0.1372	-0.2548	-0.1337	0.5156	0.1465	0.5452	0.0886	-0.089	-0.0399	-0.0614	-0.1037	-0.4312	-0.0843	0.1603	-0.0161	0.1104	0.0142	-0.0301	0.1793	0.0133	0.3353	7.68	-1.4941	15.6525
23	0.0097	0.0213	-0.0318	0.0524	-0.0375	0.1208	-0.1856	0.0704	-0.0107	-0.0563	0.3005	0.0076	-0.0141	-0.1433	0.0022	0.1446	-0.0168	-0.0239	0.208	-0.0058	0.1781	-8.0909	3.0783	12.6686
24	0.1613	0.0375	-0.1178	0.0654	0.0875	0.4142	0.0533	-0.2255	-0.1918	0.3352	-0.1509	-0.3964	0.1608	-0.079	-0.413	0.2204	-0.0196	-0.131	0.2091	0.0185	0.2506	1.387	-2.8494	24.3909
25	0.0217	0.0164	-0.0121	0.0625	0.0186	0.0161	0.0077	-0.3259	0.1739	0.359	0.042	-0.1441	-0.041	-0.0842	0.0001	0.2309	0.004	-0.0568	0.2482	-0.0338	0.2708	-2.2512	7.3655	26.1963
26	0.2578	0.3633	-0.2417	0.6709	-0.2397	0.2873	-0.0247	-0.2126	-0.1936	0.3802	-0.136	-0.3798	0.0966	-0.061	-0.1529	0.2045	-0.0139	-0.0671	0.229	0.0356	0.2525	-4.2456	-7.1306	24.0663
27	0.0167	-0.0191	-0.0546	0.1784	0.0874	0.1924	-0.2064	-0.0173	0.1184	-0.1231	0.0511	-0.2941	-0.1638	0.0771	-0.0321	0.1374	-0.033	-0.0148	0.1534	-0.0056	0.3667	6.401	7.5175	6.672

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 253 through 260 )	A	253 - 260
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 261 through 276 )	A	261 - 276
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 277 through 296 )	A	277 - 296
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 297 through 310 )	A	297 - 310
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 311 through 320 )	A	311 - 320
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 321 through 330 )	A	321 - 330
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 331 through 342 )	A	331 - 342
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 343 through 367 )	A	343 - 367
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 368 through 375 )	A	368 - 375
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 376 through 384 )	A	376 - 384
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 253 through 260 )	B	253 - 260
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 261 through 276 )	B	261 - 276
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 277 through 296 )	B	277 - 296
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 297 through 310 )	B	297 - 310
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 311 through 320 )	B	311 - 320
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 321 through 330 )	B	321 - 330
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 331 through 342 )	B	331 - 342
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 343 through 375 )	B	343 - 375
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 376 through 384 )	B	376 - 384
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 253 through 260 )	C	253 - 260
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 261 through 276 )	C	261 - 276
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 277 through 296 )	C	277 - 296
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 297 through 310 )	C	297 - 310
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 311 through 330 )	C	311 - 330
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 331 through 342 )	C	331 - 342
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 343 through 375 )	C	343 - 375
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 376 through 384 )	C	376 - 384

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