5J4T - JenaLib

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Title :   STRUCTURE OF TETRAMERIC JACALIN COMPLEXED WITH GLCNAC BETA-(1,3) GAL-BETA-OME

Authors :   K. V. Abhinav, K. Sharma, A. Surolia, M. Vijayan

Date :   01 Apr 16 (Deposition) - 08 Feb 17 (Release) - 08 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: E,F,G,H  (1x)

Keywords :   Plant Lectins, Sugar Binding Protein, Galactose Specific Lectin, Beta-Prism I Fold, Post Translational Proteolysis, T-Antigen Binding Protein, Reducing And Non-Reducing Sugars (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. V. Abhinav, K. Sharma, A. Surolia, M. Vijayan
Distortion Of The Ligand Molecule As A Strategy For Modulating Binding Affinity: Further Studies Involving Complexes Of Jacalin With Beta-Substituted Disaccharides.
Iubmb Life V. 69 72 2017
PubMed-ID: 28111895 | Reference-DOI: 10.1002/IUB.1593

Molecule 1 - AGGLUTININ ALPHA CHAIN
	Chains	:	A, C, E, G
	Organ	:	SEED
	Organism Common	:	JACK FRUIT
	Organism Scientific	:	ARTOCARPUS INTEGER
	Organism Taxid	:	3490
	Synonym	:	JACALIN ALPHA CHAIN

Molecule 2 - AGGLUTININ BETA-3 CHAIN
	Chains	:	B, D, F, H
	Organ	:	SEED
	Organism Common	:	JACK FRUIT
	Organism Scientific	:	ARTOCARPUS INTEGER
	Organism Taxid	:	3490
	Synonym	:	JACALIN BETA-3 CHAIN

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:					E	F	G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 12)

No.	Name	Count	Type	Full Name
1	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
2	MBG	2	Ligand/Ion	METHYL-BETA-GALACTOSE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	MBG	1	Ligand/Ion	METHYL-BETA-GALACTOSE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	MBG	1	Ligand/Ion	METHYL-BETA-GALACTOSE
3	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PRO A:53 , HOH A:304	binding site for residue EDO A 201
02	AC2	SOFTWARE	ASN A:110 , GLY A:111 , LEU A:112 , GLN F:3 , SER F:4	binding site for residue EDO A 202
03	AC3	SOFTWARE	ASP A:59 , SER A:62	binding site for residue EDO A 203
04	AC4	SOFTWARE	TYR C:39 , VAL C:40 , SER E:18 , ASP E:27 , LYS E:45	binding site for residue EDO E 201
05	AC5	SOFTWARE	ALA E:3 , PHE E:4 , ASP E:5 , LYS E:117 , GLY E:118 , TYR E:126	binding site for residue PEG E 202
06	AC6	SOFTWARE	THR E:102 , TRP F:15 , GLY F:16 , HOH F:202 , ASN G:105	binding site for residue EDO F 101
07	AC7	SOFTWARE	TYR C:78 , VAL C:79 , GLY G:1 , TYR G:78 , GLY G:121 , TYR G:122 , TRP G:123 , ASP G:125 , HOH G:309	binding site for residue MBG G 201
08	AC8	SOFTWARE	ALA G:3 , PHE G:4 , LYS G:117 , GLY G:118 , HOH G:301	binding site for residue EDO G 202
09	AC9	SOFTWARE	SER G:46 , PHE G:47	binding site for residue EDO G 203
10	AD1	SOFTWARE	ASN E:105 , THR G:72 , THR G:102 , TRP H:15 , GLY H:16 , HOH H:202 , HOH H:207	binding site for residue EDO H 101
11	AD2	SOFTWARE	GLY A:1 , PHE A:47 , TYR A:78 , GLY A:121 , TYR A:122 , TRP A:123 , ASP A:125 , HOH A:305 , HOH A:306 , HOH A:308 , HOH A:338	binding site for Poly-Saccharide residues NAG A 204 through MBG A 205

(no "SS Bond" information available for 5J4T)

Asymmetric Unit

No.	Residues
1	Phe A:60	-	Pro A:61
2	Gly A:94	-	Pro A:95
3	Gly B:13	-	Pro B:14
4	Phe C:60	-	Pro C:61
5	Gly C:94	-	Pro C:95
6	Gly D:13	-	Pro D:14
7	Phe E:60	-	Pro E:61
8	Gly E:94	-	Pro E:95
9	Gly F:13	-	Pro F:14
10	Phe G:60	-	Pro G:61
11	Gly G:94	-	Pro G:95
12	Gly H:13	-	Pro H:14

(no "SAP(SNP)/Variant" information available for 5J4T)

(no "PROSITE Motif" information available for 5J4T)

(no "Exon" information available for 5J4T)

Asymmetric 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
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Chain A from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j4t A   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 5j4t B   3 QSGISQTVIVGPWGAK  18
                                    12

Chain C from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeeeeeee.......eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j4t C   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain D from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 5j4t D   3 QSGISQTVIVGPWG  16
                                    12

Chain E from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeeeeeee.......eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j4t E   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain F from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 5j4t F   3 QSGISQTVIVGPWGAK  18
                                    12

Chain G from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeee.....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j4t G   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain H from PDB  Type:PROTEIN  Length:15
                                               
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 5j4t H   4 SGISQTVIVGPWGAK  18
                                    13

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 '\|'

(no "SCOP Domain" information available for 5J4T)

(no "CATH Domain" information available for 5J4T)

(no "Pfam Domain" information available for 5J4T)

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly A:94 - Pro A:95	[ RasMol ]
		Gly B:13 - Pro B:14	[ RasMol ]
		Gly C:94 - Pro C:95	[ RasMol ]
		Gly D:13 - Pro D:14	[ RasMol ]
		Gly E:94 - Pro E:95	[ RasMol ]
		Gly F:13 - Pro F:14	[ RasMol ]
		Gly G:94 - Pro G:95	[ RasMol ]
		Gly H:13 - Pro H:14	[ RasMol ]
		Phe A:60 - Pro A:61	[ RasMol ]
		Phe C:60 - Pro C:61	[ RasMol ]
		Phe E:60 - Pro E:61	[ RasMol ]
		Phe G:60 - Pro G:61	[ RasMol ]

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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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