1K7T - JenaLib

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Title :   CRYSTAL STRUCTURE ANALYSIS OF CROSSLINKED-WGA3/GLCNACBETA1,6GAL COMPLEX

Authors :   M. Muraki, M. Ishimura, K. Harata

Date :   22 Oct 01 (Deposition) - 03 Apr 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Hevein-Type Fold, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Muraki, M. Ishimura, K. Harata
Interactions Of Wheat-Germ Agglutinin With Glcnac Beta 1, 6Gal Sequence
Biochim. Biophys. Acta V. 1569 10 2002
PubMed-ID: 11853952 | Reference-DOI: 10.1016/S0304-4165(01)00231-8
(for further references see the PDB file header)

Molecule 1 - AGGLUTININ ISOLECTIN 3
	Chains	:	A, B
	Organism Common	:	BREAD WHEAT
	Organism Scientific	:	TRITICUM AESTIVUM
	Organism Taxid	:	4565
	Synonym	:	WGA3

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:62 , TYR A:64 , HIS A:66 , TYR A:73 , GAL A:188 , GLU B:115	BINDING SITE FOR RESIDUE NAG A 187
2	AC2	SOFTWARE	TYR A:64 , NAG A:187	BINDING SITE FOR RESIDUE GAL A 188
3	AC3	SOFTWARE	SER A:114 , GLU A:115 , SER B:62 , TYR B:64 , HIS B:66 , GLU B:72 , TYR B:73 , GAL B:188 , HOH B:192	BINDING SITE FOR RESIDUE NAG B 187
4	AC4	SOFTWARE	TYR A:23 , GLU A:115 , TYR B:64 , NAG B:187	BINDING SITE FOR RESIDUE GAL B 188

Asymmetric/Biological Unit

No.	Residues
1	A:3	-	A:18
2	A:12	-	A:24
3	A:17	-	A:31
4	A:35	-	A:40
5	A:46	-	A:61
6	A:55	-	A:67
7	A:60	-	A:74
8	A:78	-	A:83
9	A:89	-	A:104
10	A:98	-	A:110
11	A:103	-	A:117
12	A:121	-	A:126
13	A:132	-	A:147
14	A:141	-	A:153
15	A:146	-	A:160
16	A:164	-	A:169
17	B:3	-	B:18
18	B:12	-	B:24
19	B:17	-	B:31
20	B:35	-	B:40
21	B:46	-	B:61
22	B:55	-	B:67
23	B:60	-	B:74
24	B:78	-	B:83
25	B:89	-	B:104
26	B:98	-	B:110
27	B:103	-	B:117
28	B:121	-	B:126
29	B:132	-	B:147
30	B:141	-	B:153
31	B:146	-	B:160
32	B:164	-	B:169

(no "Cis Peptide Bond" information available for 1K7T)

(no "SAP(SNP)/Variant" information available for 1K7T)

Asymmetric/Biological Unit (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHIT_BIND_I_2	PS50941	Chitin-binding type-1 domain profile.	AGI3_WHEAT	1-42 43-85 86-128 129-171	8	A:2-42 B:2-42 A:43-85 B:43-85 A:86-128 B:86-128 A:129-171 B:129-171
2	CHIT_BIND_I_1	PS00026	Chitin recognition or binding domain signature.	AGI3_WHEAT	12-31 55-74 98-117 141-160	8	A:12-31 B:12-31 A:55-74 B:55-74 A:98-117 B:98-117 A:141-160 B:141-160

(no "Exon" information available for 1K7T)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:171
 aligned with AGI3_WHEAT | P10969 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 
           AGI3_WHEAT     1 QRCGEQGSGMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGKTCPNNHCCSQYGHCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGYCGLGSEFCGEGCQNGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 171
               SCOP domains d1k7ta1 A:1-52 Wheat germ agglutinin (WGA)          d1k7ta2 A:53-86                   d1k7ta3 A:87-129                           d1k7ta4 A:130-171                          SCOP domains
               CATH domains -1k7tA01 A:2-42                           1k7tA02 A:43-85                            1k7tA03 A:86-128                           1k7tA04 A:129-171                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhee.....eeeehhhhh..............hhhhh...hhhhhee.....ee..................................ee.....ee.hhhhhh...........................ee.....ee.hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CHIT_BIND_I_2  PDB: A:2-42 UniProt: 1-42  CHIT_BIND_I_2  PDB: A:43-85 UniProt: 43-85 CHIT_BIND_I_2  PDB: A:86-128               CHIT_BIND_I_2  PDB: A:129-171               PROSITE (1)
                PROSITE (2) -----------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       ----------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k7t A   1 xRCGEQGSGMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGKTCPNNHCCSQYGHCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGYCGLGSEFCGEGCQNGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 171
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 
                            |                                                                                                                                                                          
                            1-PCA

Chain B from PDB  Type:PROTEIN  Length:171
 aligned with AGI3_WHEAT | P10969 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 
           AGI3_WHEAT     1 QRCGEQGSGMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGKTCPNNHCCSQYGHCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGYCGLGSEFCGEGCQNGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 171
               SCOP domains d1k7tb1 B:1-52 Wheat germ agglutinin (WGA)          d1k7tb2 B:53-86                   d1k7tb3 B:87-129                           d1k7tb4 B:130-171                          SCOP domains
               CATH domains -1k7tB01 B:2-42                           1k7tB02 B:43-85                            1k7tB03 B:86-128                           1k7tB04 B:129-171                           CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-1k7tB01 B:129-169          -- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-1k7tB02 B:129-169          -- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-1k7tB03 B:129-169          -- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-1k7tB04 B:129-169          -- Pfam domains (4)
           Pfam domains (5) --------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-1k7tB05 B:129-169          -- Pfam domains (5)
           Pfam domains (6) --------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-1k7tB06 B:129-169          -- Pfam domains (6)
           Pfam domains (7) --------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-1k7tB07 B:129-169          -- Pfam domains (7)
           Pfam domains (8) --------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-1k7tB08 B:129-169          -- Pfam domains (8)
         Sec.struct. author ..hhhhhh........ee.....ee.hhhhhh......................hhhhhee.....ee.hhhhhh...........................ee.....ee.hhhhhh..............hhhhh........ee.....eeehhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CHIT_BIND_I_2  PDB: B:2-42 UniProt: 1-42  CHIT_BIND_I_2  PDB: B:43-85 UniProt: 43-85 CHIT_BIND_I_2  PDB: B:86-128               CHIT_BIND_I_2  PDB: B:129-171               PROSITE (1)
                PROSITE (2) -----------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       ----------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k7t B   1 xRCGEQGSGMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGKTCPNNHCCSQYGHCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGYCGLGSEFCGEGCQNGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 171
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 
                            1-PCA

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Knottins (small inhibitors, toxins, lectins) (761)

Superfamily: Plant lectins/antimicrobial peptides (31)

Family: Hevein-like agglutinin (lectin) domain (28)

Protein domain: Wheat germ agglutinin (WGA) (12)

Wheat (Triticum aestivum), also known as Triticum vulgare [TaxId: 4565] (12)

1a	d1k7ta1	A:1-52
1b	d1k7ta2	A:53-86
1c	d1k7ta3	A:87-129
1d	d1k7ta4	A:130-171
1e	d1k7tb1	B:1-52
1f	d1k7tb2	B:53-86
1g	d1k7tb3	B:87-129
1h	d1k7tb4	B:130-171

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Wheat Germ Agglutinin (Isolectin 2); domain 1 (140)

Homologous Superfamily: [code=3.30.60.10, no name defined] (23)

Bread wheat (Triticum aestivum) (10)

1a	1k7tA02	A:43-85
1b	1k7tB02	B:43-85
1c	1k7tA03	A:86-128
1d	1k7tB03	B:86-128
1e	1k7tA01	A:2-42
1f	1k7tB01	B:2-42
1g	1k7tA04	A:129-171
1h	1k7tB04	B:129-171

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Chitin_bind_1] (17)

Family: Chitin_bind_1 (17)

Triticum aestivum (Wheat) (8)

1a	Chitin_bind_1-1k7tB01	B:129-169
1b	Chitin_bind_1-1k7tB02	B:129-169
1c	Chitin_bind_1-1k7tB03	B:129-169
1d	Chitin_bind_1-1k7tB04	B:129-169
1e	Chitin_bind_1-1k7tB05	B:129-169
1f	Chitin_bind_1-1k7tB06	B:129-169
1g	Chitin_bind_1-1k7tB07	B:129-169
1h	Chitin_bind_1-1k7tB08	B:129-169

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (AGI3_WHEAT | P10969)

molecular function
	GO:0030246		carbohydrate binding		Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0008061		chitin binding		Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.

Asymmetric/Biological Unit
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UniProtKB/Swiss-Prot
	AGI3_WHEAT \| P10969	:	1k7u 1k7v 1wgt 2x52

1k7u	1K7U CONTAINS CROSSLINKED-WGA3/GLCNACBETA1,4GLCNAC COMPLEX
1k7v	1K7V CONTAINS CROSSLINKED-WGA3/GLCNACBETA1,6GALBETA1,4GLC
1wgt	1WGT CONTAINS WHEAT-GERM-AGGLUTININ ISOLECTIN-3(WGA3)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (4, 4)

SS Bonds (32, 32)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 16)

Exons (0, 0)

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SCOP Domains (1, 8)

CATH Domains (1, 8)

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