PDB-2wnl: CRYSTAL STRUCTURE OF APLYSIA ACHBP IN COMPLEX WITH ANABASEINE

ID or keywords:

Entry

Database: PDB / ID: 2wnl

Title

CRYSTAL STRUCTURE OF APLYSIA ACHBP IN COMPLEX WITH ANABASEINE

Components

SOLUBLE ACETYLCHOLINE RECEPTOR

Keywords

RECEPTOR / ANABASEINE / ACETYLCHOLINE BINDING PROTEIN

Function / homology

Function and homology information

acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / postsynapse / neuron projection / identical protein binding / membrane / metal ion binding
Similarity search - Function

Biological species

APLYSIA CALIFORNICA (California sea hare)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Sulzenbacher, G. / Hibbs, R. / Shi, J. / Talley, T. / Conrod, S. / Kem, W. / Taylor, P. / Marchot, P. / Bourne, Y.

Citation

Journal: EMBO J. / Year: 2009
Title: Structural determinants for interaction of partial agonists with acetylcholine binding protein and neuronal alpha7 nicotinic acetylcholine receptor.
Authors: Hibbs, R.E. / Sulzenbacher, G. / Shi, J. / Talley, T.T. / Conrod, S. / Kem, W.R. / Taylor, P. / Marchot, P. / Bourne, Y.

History

Deposition	Jul 9, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 1, 2009	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 2.0	Nov 21, 2018	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type Item: _atom_site.label_alt_id / _citation.journal_abbrev ..._atom_site.label_alt_id / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _struct_conn_type.id
Revision 2.1	Apr 3, 2019	Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 2.2	Jul 29, 2020	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wn/2wnl ftp://data.pdbj.org/pub/pdb/validation_reports/wn/2wnl	HTTPS FTP

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Related structure data

Related structure data	2wn9C 2wncC 2wnjC 2bynS 2br7 2br8 2byp 2byq 2byr 2bys 2c9t 2uz6 2w8f 2w8g 2y7y C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4frr-1 4frr-2 2wnc-d 2byr-2 2wzy-1 2wzy-2 5tsf-d 2x00-d 3c79-d 4xk9-2 5tvh-d 5brx-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (4) #71 - Nov 2005 Acetylcholine Receptor similarity (4)

Deposited unit

A: SOLUBLE ACETYLCHOLINE RECEPTOR

B: SOLUBLE ACETYLCHOLINE RECEPTOR

C: SOLUBLE ACETYLCHOLINE RECEPTOR

D: SOLUBLE ACETYLCHOLINE RECEPTOR

E: SOLUBLE ACETYLCHOLINE RECEPTOR

F: SOLUBLE ACETYLCHOLINE RECEPTOR

G: SOLUBLE ACETYLCHOLINE RECEPTOR

H: SOLUBLE ACETYLCHOLINE RECEPTOR

I: SOLUBLE ACETYLCHOLINE RECEPTOR

J: SOLUBLE ACETYLCHOLINE RECEPTOR

hetero molecules

261 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

F: SOLUBLE ACETYLCHOLINE RECEPTOR

G: SOLUBLE ACETYLCHOLINE RECEPTOR

H: SOLUBLE ACETYLCHOLINE RECEPTOR

I: SOLUBLE ACETYLCHOLINE RECEPTOR

J: SOLUBLE ACETYLCHOLINE RECEPTOR

hetero molecules

defined by author&software
130 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: SOLUBLE ACETYLCHOLINE RECEPTOR

B: SOLUBLE ACETYLCHOLINE RECEPTOR

C: SOLUBLE ACETYLCHOLINE RECEPTOR

D: SOLUBLE ACETYLCHOLINE RECEPTOR

E: SOLUBLE ACETYLCHOLINE RECEPTOR

hetero molecules

defined by author&software
131 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	84.251, 125.768, 257.001
Angle α, β, γ (deg.)	90.00, 95.40, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	E
5	1	F
6	1	G
7	1	H
8	1	I
9	1	J
1	2	A
2	2	D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 22 - 180 / Label seq-ID: 30 - 188

Dom-ID	Ens-ID	Refine code	Auth asym-ID	Label asym-ID
1	1	3	A	A
2	1	3	B	B
3	1	3	C	C
4	1	3	E	E
5	1	3	F	F
6	1	3	G	G
7	1	3	H	H
8	1	3	I	I
9	1	3	J	J
1	2	5	A	A
2	2	5	D	D

NCS ensembles :

ID
1
2

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Protein / Sugars , 2 types, 13 molecules ABCDEFGHIJ

#1: Protein

SOLUBLE ACETYLCHOLINE RECEPTOR / ACETYLCHOLINE BINDING PROTEIN

Mass: 25852.744 Da / Num. of mol.: 10 / Fragment: RESIDUES 18-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

APLYSIA CALIFORNICA (California sea hare)
Cell: SENSORY CELL / Cell line (production host): HEK293 / Production host:

HOMO SAPIENS (human) / References: UniProt: Q8WSF8

#6: 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: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 5 types, 320 molecules

#2: Chemical	ChemComp-AN4 / 3,4,5,6-tetrahydro-2,3'-bipyridine / anabaseine Mass: 160.216 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₀H₁₂N₂ / Comment: alkaloid, toxin*YM
#3: Chemical	ChemComp-AN5 / 5-amino-1-pyridin-3-ylpentan-1-one Mass: 178.231 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₂O
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54 % / Description: NONE
Crystal grow	Details: 19% PEG4000, 95 MM NA-CITRATE, PH 5.6, 19% ISOPROPANOL, 5% GLYCEROL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 5, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.872 Å / Relative weight: 1
Reflection	Resolution: 2.7→70 Å / Num. obs: 73265 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / B_iso Wilson estimate: 47.82 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 9.8
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0102	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BYN

2byn

Resolution: 2.7→258.2 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.889 / SU B: 27.976 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 2.215 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GLOBAL B-FACTORS, CONTAINING RESIDUAL AND TLS COMPONENT HAVE BEEN DEPOSITED.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25059	2199	3 %	RANDOM
R_work	0.2018	-	-	-
obs	0.20327	70727	99.54 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 40.515 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.95 Å²	-0 Å²	0.43 Å²
2-	-	2.63 Å²	-0 Å²
3-	-	-	-3.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→258.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16874	0	170	307	17351

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	17541
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	11715
X-RAY DIFFRACTION	r_angle_refined_deg	1.108	1.959	23899
X-RAY DIFFRACTION	r_angle_other_deg	0.897	3	28532
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.121	5	2118
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.264	24.33	836
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.18	15	2841
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.432	15	107
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	2645
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	19447
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3560
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.555	2.5	10623
X-RAY DIFFRACTION	r_mcbond_other	0.06	2.5	4191
X-RAY DIFFRACTION	r_mcangle_it	1.031	3.5	17357
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.955	2.5	6918
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.542	3.5	6534
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	934	tight positional	0.19	0.4
1	2	B	934	tight positional	0.2	0.4
1	3	C	934	tight positional	0.17	0.4
1	4	E	934	tight positional	0.23	0.4
1	5	F	934	tight positional	0.2	0.4
1	6	G	934	tight positional	0.24	0.4
1	7	H	934	tight positional	0.24	0.4
1	8	I	934	tight positional	0.32	0.4
1	9	J	934	tight positional	0.2	0.4
2	1	A	938	medium positional	0.17	0.8
2	2	D	938	medium positional	0.17	0.8
1	1	A	1097	loose positional	0.58	10
1	2	B	1097	loose positional	0.53	10
1	3	C	1097	loose positional	0.65	10
1	4	E	1097	loose positional	0.64	10
1	5	F	1097	loose positional	0.52	10
1	6	G	1097	loose positional	0.59	10
1	7	H	1097	loose positional	0.57	10
1	8	I	1097	loose positional	0.75	10
1	9	J	1097	loose positional	0.61	10
2	1	A	1133	loose positional	0.43	10
2	2	D	1133	loose positional	0.43	10
1	1	A	934	tight thermal	0.04	0.5
1	2	B	934	tight thermal	0.03	0.5
1	3	C	934	tight thermal	0.03	0.5
1	4	E	934	tight thermal	0.03	0.5
1	5	F	934	tight thermal	0.04	0.5
1	6	G	934	tight thermal	0.03	0.5
1	7	H	934	tight thermal	0.03	0.5
1	8	I	934	tight thermal	0.03	0.5
1	9	J	934	tight thermal	0.04	0.5
2	1	A	938	medium thermal	0.33	2
2	2	D	938	medium thermal	0.33	2
1	1	A	1097	loose thermal	0.03	10
1	2	B	1097	loose thermal	0.03	10
1	3	C	1097	loose thermal	0.03	10
1	4	E	1097	loose thermal	0.04	10
1	5	F	1097	loose thermal	0.04	10
1	6	G	1097	loose thermal	0.03	10
1	7	H	1097	loose thermal	0.03	10
1	8	I	1097	loose thermal	0.03	10
1	9	J	1097	loose thermal	0.03	10
2	1	A	1133	loose thermal	0.37	10
2	2	D	1133	loose thermal	0.37	10

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.365	158	-
R_work	0.308	5190	-
obs	-	-	99.93 %

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	1.4128	0.0371	0.2935	2.0687	-0.2391	1.6159	-0.0072	0.2378	0.0082	-0.112	0.0198	0.054	0.0086	-0.0233	-0.0126	0.0093	-0.0198	0.0063	0.146	-0.0506	0.0286	28.555	11.8	69.878
2	1.6422	-0.1578	0.2153	1.9485	-0.0479	2.491	0.0213	-0.0786	0.3331	0.0242	-0.0161	-0.0644	-0.3566	-0.0157	-0.0052	0.0735	-0.048	0.0146	0.1152	-0.0162	0.1095	38.533	31.802	84.723
3	1.7622	-0.3366	-0.1544	2.1285	-0.0042	1.5709	0.1146	-0.1575	0.2337	0.0632	-0.0341	0.0612	-0.1858	-0.1407	-0.0805	0.1074	-0.0426	-0.0165	0.2034	-0.0393	0.0777	30.365	29.026	110.046
4	1.5797	0.2718	-0.2703	1.5602	0.8138	2.1091	-0.0011	-0.0828	-0.0919	0.1168	-0.066	0.232	0.2397	-0.4985	0.0671	0.15	-0.1234	-0.0135	0.2899	0.037	0.0744	14.737	7.335	110.948
5	2.5232	-0.051	0.3596	1.3273	-0.4151	2.318	0.0492	-0.0418	-0.1139	0.0208	0.0322	0.1542	0.2903	-0.4704	-0.0814	0.1469	-0.137	-0.018	0.1899	-0.0303	0.1347	13.866	-3.621	85.856
6	1.6877	0.5206	0.0525	1.3757	0.1564	1.5321	0.0072	-0.3091	-0.0771	0.103	-0.0306	-0.0977	-0.0115	0.0532	0.0234	0.0471	0.0208	0.033	0.0742	0.0224	0.0636	60.889	35.526	56.992
7	1.8104	0.0836	0.0442	1.4195	0.5371	2.4447	0.0509	-0.1644	0.2125	-0.2003	0.1187	-0.2509	-0.2661	0.4572	-0.1696	0.1401	-0.0742	0.0573	0.1054	-0.0617	0.1897	76.098	52.068	42.061
8	2.6619	-1.1391	-0.9013	1.5481	0.6937	1.2256	0.1558	0.0422	0.3612	-0.2667	0.014	-0.1737	-0.2055	0.1467	-0.1698	0.285	-0.0622	0.0495	0.0549	0.0286	0.119	77.629	42.763	17.027
9	1.5736	0.4018	-0.9441	1.2518	0.283	1.8822	-0.1151	0.0721	-0.2733	-0.1251	0.0051	-0.0805	0.3382	-0.1052	0.11	0.2604	-0.0532	0.0123	0.0183	-0.0201	0.0841	63.309	20.081	16.228
10	1.4643	-0.416	0.272	1.575	-0.5312	2.7132	-0.0696	-0.0533	-0.2239	-0.1191	-0.0419	0.0065	0.4902	-0.1149	0.1115	0.1594	-0.0464	0.0542	0.0274	-0.0051	0.1552	53.02	15.763	40.982

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-4 - 207
2	X-RAY DIFFRACTION	2	B	-4 - 207
3	X-RAY DIFFRACTION	3	C	-4 - 207
4	X-RAY DIFFRACTION	4	D	-4 - 207
5	X-RAY DIFFRACTION	5	E	-4 - 207
6	X-RAY DIFFRACTION	6	F	-4 - 207
7	X-RAY DIFFRACTION	7	G	-4 - 207
8	X-RAY DIFFRACTION	8	H	-4 - 207
9	X-RAY DIFFRACTION	9	I	-4 - 207
10	X-RAY DIFFRACTION	10	J	-4 - 207

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Protein / Sugars , 2 types, 13 molecules ABCDEFGHIJ

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Non-polymers , 5 types, 320 molecules

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Protein / Sugars , 2 types, 13 molecules ABCDEFGHIJ

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