1WW5 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   AGROCYBE CYLINDRACEA GALECTIN COMPLEXED WITH 3'-SULFONYL LACTOSE

Authors :   M. Ban, H. J. Yoon, E. Demirkan, S. Utsumi, B. Mikami, F. Yagi

Date :   03 Jan 05 (Deposition) - 23 Aug 05 (Release) - 21 Jul 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Agrocybe Cylindracea Galectin, Fungal Galectin, Carbohydrate Recognition Domain, 3'-Sulfated Lactose, X-Ray Crystallographic Analysis, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Ban, H. J. Yoon, E. Demirkan, S. Utsumi, B. Mikami, F. Yagi
Structural Basis Of A Fungal Galectin From Agrocybe Cylindracea For Recognizing Sialoconjugate
J. Mol. Biol. V. 351 695 2005
PubMed-ID: 16051274 | Reference-DOI: 10.1016/J.JMB.2005.06.045
(for further references see the PDB file header)

Molecule 1 - GALECTIN
	Chains	:	A, B, C, D
	Organism Scientific	:	AGROCYBE CYLINDRACEA
	Organism Taxid	:	64608

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	BGC	4	Ligand/Ion	BETA-D-GLUCOSE
2	SGA	4	Ligand/Ion	O3-SULFONYLGALACTOSE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
2	SGA	2	Ligand/Ion	O3-SULFONYLGALACTOSE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
2	SGA	2	Ligand/Ion	O3-SULFONYLGALACTOSE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:46 , HIS A:62 , ARG A:66 , ASN A:75 , TRP A:83 , GLU A:86 , BGC A:201 , HOH A:1040	BINDING SITE FOR RESIDUE SGA A 200
2	AC2	SOFTWARE	ARG A:66 , GLU A:86 , ARG A:88 , SGA A:200 , HOH A:1314	BINDING SITE FOR RESIDUE BGC A 201
3	AC3	SOFTWARE	ASN B:46 , HIS B:62 , ARG B:66 , ASN B:75 , TRP B:83 , GLU B:86 , BGC B:211 , HOH B:810	BINDING SITE FOR RESIDUE SGA B 210
4	AC4	SOFTWARE	ARG B:66 , GLU B:86 , ARG B:88 , SGA B:210 , HOH B:889	BINDING SITE FOR RESIDUE BGC B 211
5	AC5	SOFTWARE	ASN C:46 , HIS C:62 , ARG C:66 , ASN C:75 , TRP C:83 , GLU C:86 , BGC C:221 , HOH C:1085	BINDING SITE FOR RESIDUE SGA C 220
6	AC6	SOFTWARE	HOH B:1341 , ARG C:66 , GLU C:86 , ARG C:88 , SGA C:220	BINDING SITE FOR RESIDUE BGC C 221
7	AC7	SOFTWARE	ASN D:46 , HIS D:62 , ARG D:66 , ASN D:75 , TRP D:83 , GLU D:86 , BGC D:231 , HOH D:855	BINDING SITE FOR RESIDUE SGA D 230
8	AC8	SOFTWARE	ARG D:66 , GLU D:86 , ARG D:88 , SGA D:230	BINDING SITE FOR RESIDUE BGC D 231

(no "SS Bond" information available for 1WW5)

Asymmetric Unit

No.	Residues
1	Ser A:44	-	Pro A:45
2	Ser B:44	-	Pro B:45
3	Ser C:44	-	Pro C:45
4	Ser D:44	-	Pro D:45

(no "SAP(SNP)/Variant" information available for 1WW5)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	ATLE_AGRAE	12-155	4	A:16-158 B:16-158 C:16-158 D:16-158

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	ATLE_AGRAE	12-155	2	A:16-158 - - D:16-158

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	ATLE_AGRAE	12-155	2	- B:16-158 C:16-158 -

(no "Exon" information available for 1WW5)

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
	(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:160
 aligned with ATLE_AGRAE | Q6WY08 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:160
                              1                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158
           ATLE_AGRAE     - --QGVNIYNISAGTSVDLAAPVTTGDIVTFFSSALNLNAGAGNPNNTTLNLFAENGAYLLHIAFRLQENVIIFNSRQPDGPWLVEQRVSDVANQFAGIDGKAMVTVFDHGDKYQVVINEKTVIQYTKQISGLTLSLSYNATEETSIFSTVVEAVTYTGLA 158
               SCOP domains d1ww5a_ A: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeee....eeeeee..............eeeeee.....eeeeeeee....eeeeeee.........eeee.hhhhh......eeeeeee...eeeeee..eeeeeee......eeeeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------GALECTIN  PDB: A:16-158 UniProt: 12-155                                                                                                         --- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ww5 A   2 TTSAVNIYNISAGASVDLAAPVTTGDIVTFFSSALNLSAGAGSPNNTALNLLSENGAYLLHIAFRLQENVIVFNSRQPNAPWLVEQRVSNVANQFIGSGGKAMVTVFDHGDKYQVVINEKTVIQYTKQISGTTSSLSYNSTEGTSIFSTVVEAVTYTGLA 161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with ATLE_AGRAE | Q6WY08 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:160
                              1                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158
           ATLE_AGRAE     - --QGVNIYNISAGTSVDLAAPVTTGDIVTFFSSALNLNAGAGNPNNTTLNLFAENGAYLLHIAFRLQENVIIFNSRQPDGPWLVEQRVSDVANQFAGIDGKAMVTVFDHGDKYQVVINEKTVIQYTKQISGLTLSLSYNATEETSIFSTVVEAVTYTGLA 158
               SCOP domains d1ww5b_ B: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeee....eeeeee..............eeeeee.....eeeeeeee....eeeeeee.........eeee.hhhhh......eeeeeee...eeeeee..eeeeeee......eeeeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------GALECTIN  PDB: B:16-158 UniProt: 12-155                                                                                                         --- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ww5 B   2 TTSAVNIYNISAGASVDLAAPVTTGDIVTFFSSALNLSAGAGSPNNTALNLLSENGAYLLHIAFRLQENVIVFNSRQPNAPWLVEQRVSNVANQFIGSGGKAMVTVFDHGDKYQVVINEKTVIQYTKQISGTTSSLSYNSTEGTSIFSTVVEAVTYTGLA 161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain C from PDB  Type:PROTEIN  Length:160
 aligned with ATLE_AGRAE | Q6WY08 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:160
                              1                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158
           ATLE_AGRAE     - --QGVNIYNISAGTSVDLAAPVTTGDIVTFFSSALNLNAGAGNPNNTTLNLFAENGAYLLHIAFRLQENVIIFNSRQPDGPWLVEQRVSDVANQFAGIDGKAMVTVFDHGDKYQVVINEKTVIQYTKQISGLTLSLSYNATEETSIFSTVVEAVTYTGLA 158
               SCOP domains d1ww5c_ C: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeee....eeeeee..............eeeeee.....eeeeeeee....eeeeeee.........eeee.hhhhh......eeeeeee...eeeeee..eeeeeee......eeeeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------GALECTIN  PDB: C:16-158 UniProt: 12-155                                                                                                         --- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ww5 C   2 TTSAVNIYNISAGASVDLAAPVTTGDIVTFFSSALNLSAGAGSPNNTALNLLSENGAYLLHIAFRLQENVIVFNSRQPNAPWLVEQRVSNVANQFIGSGGKAMVTVFDHGDKYQVVINEKTVIQYTKQISGTTSSLSYNSTEGTSIFSTVVEAVTYTGLA 161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain D from PDB  Type:PROTEIN  Length:160
 aligned with ATLE_AGRAE | Q6WY08 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:160
                              1                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158
           ATLE_AGRAE     - --QGVNIYNISAGTSVDLAAPVTTGDIVTFFSSALNLNAGAGNPNNTTLNLFAENGAYLLHIAFRLQENVIIFNSRQPDGPWLVEQRVSDVANQFAGIDGKAMVTVFDHGDKYQVVINEKTVIQYTKQISGLTLSLSYNATEETSIFSTVVEAVTYTGLA 158
               SCOP domains d1ww5d_ D: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------Gal-bind_lectin-1ww5D01 D:14-144                                                                                                   ----------------- Pfam domains (1)
           Pfam domains (2) ------------Gal-bind_lectin-1ww5D02 D:14-144                                                                                                   ----------------- Pfam domains (2)
           Pfam domains (3) ------------Gal-bind_lectin-1ww5D03 D:14-144                                                                                                   ----------------- Pfam domains (3)
           Pfam domains (4) ------------Gal-bind_lectin-1ww5D04 D:14-144                                                                                                   ----------------- Pfam domains (4)
         Sec.struct. author ...eeeeeeee..eeeeeeeee....eeeeee..............eeeeee.....eeeeeeee....eeeeeee.........eeee.hhhhh......eeeeeee...eeeeee..eeeeeee......eeeeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------GALECTIN  PDB: D:16-158 UniProt: 12-155                                                                                                         --- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ww5 D   2 TTSAVNIYNISAGASVDLAAPVTTGDIVTFFSSALNLSAGAGSPNNTALNLLSENGAYLLHIAFRLQENVIVFNSRQPNAPWLVEQRVSNVANQFIGSGGKAMVTVFDHGDKYQVVINEKTVIQYTKQISGTTSSLSYNSTEGTSIFSTVVEAVTYTGLA 161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: automated matches (133)

Protein domain: automated matches (133)

Agrocybe cylindracea [TaxId: 64608] (6)

1a	d1ww5a_	A:
1b	d1ww5c_	C:
1c	d1ww5d_	D:
1d	d1ww5b_	B:

(no "CATH Domain" information available for 1WW5)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Gal-bind_lectin (60)

Agrocybe aegerita (Black poplar mushroom) (13)

1a	Gal-bind_lectin-1ww5D01	D:14-144
1b	Gal-bind_lectin-1ww5D02	D:14-144
1c	Gal-bind_lectin-1ww5D03	D:14-144
1d	Gal-bind_lectin-1ww5D04	D:14-144

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ATLE_AGRAE | Q6WY08)

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:0004536	deoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0030247	polysaccharide binding	Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
biological process
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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	Cis Peptide Bonds
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		Ser D:44 - Pro D:45	[ RasMol ]

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	1ww5
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1ww4	THE SAME PROTEIN COMPLEXED WITH N-ACETYLNEURAMINYL LACTOSE
1ww6	THE SAME PROTEIN COMPLEXED WITH LACTOSE
1ww7	THE SAME PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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