3WCR - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PLANT LECTIN (LIGAND-FREE FORM)

Authors :   M. Nagae, Y. Yamaguchi

Date :   31 May 13 (Deposition) - 09 Apr 14 (Release) - 09 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Legume Lectin Fold, Carbohydrate Binding, N-Glycan, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Nagae, K. Soga, K. Morita-Matsumoto, S. Hanashima, A. Ikeda, K. Yamamoto, Y. Yamaguchi
Phytohemagglutinin From Phaseolus Vulgaris (Pha-E) Displays A Novel Glycan Recognition Mode Using A Common Legume Lecti Fold
Glycobiology V. 24 368 2014
PubMed-ID: 24436051 | Reference-DOI: 10.1093/GLYCOB/CWU004

Molecule 1 - ERYTHROAGGLUTININ
	Chains	:	A, B
	Fragment	:	UNP RESIDUES 22-275
	Organism Common	:	KIDNEY BEAN
	Organism Scientific	:	PHASEOLUS VULGARIS
	Organism Taxid	:	3885
	Synonym	:	PHYTOHEMAGGLUTININ

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 21)

No.	Name	Count	Type	Full Name
1	BR	19	Ligand/Ion	BROMIDE ION
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:92 , SER A:248	BINDING SITE FOR RESIDUE BR A 1002
02	AC2	SOFTWARE	LYS A:180	BINDING SITE FOR RESIDUE BR A 1003
03	AC3	SOFTWARE	PRO A:62 , ASN B:59	BINDING SITE FOR RESIDUE BR A 1004
04	AC4	SOFTWARE	THR A:173 , THR A:174 , THR A:175	BINDING SITE FOR RESIDUE BR A 1005
05	AC5	SOFTWARE	GLY A:125	BINDING SITE FOR RESIDUE BR A 1006
06	AC6	SOFTWARE	ILE A:236 , THR A:237	BINDING SITE FOR RESIDUE BR A 1007
07	AC7	SOFTWARE	TRP A:225 , NAG B:1001	BINDING SITE FOR RESIDUE BR A 1008
08	AC8	SOFTWARE	ASN A:33 , GLU A:34 , NAG A:1001	BINDING SITE FOR RESIDUE BR A 1009
09	AC9	SOFTWARE	THR A:25 , GLN A:77 , HOH B:1104	BINDING SITE FOR RESIDUE BR A 1010
10	BC1	SOFTWARE	TYR A:133 , ARG B:41	BINDING SITE FOR RESIDUE BR B 1002
11	BC2	SOFTWARE	ASN A:132 , GLN B:40 , PRO B:120	BINDING SITE FOR RESIDUE BR B 1003
12	BC3	SOFTWARE	GLN B:119 , LYS B:121	BINDING SITE FOR RESIDUE BR B 1004
13	BC4	SOFTWARE	NAG A:1001 , GLU B:224 , TRP B:225	BINDING SITE FOR RESIDUE BR B 1005
14	BC5	SOFTWARE	ILE B:236 , THR B:237	BINDING SITE FOR RESIDUE BR B 1006
15	BC6	SOFTWARE	GLU B:34 , NAG B:1001	BINDING SITE FOR RESIDUE BR B 1007
16	BC7	SOFTWARE	SER B:92 , SER B:248 , TRP B:249 , SER B:250	BINDING SITE FOR RESIDUE BR B 1009
17	BC8	SOFTWARE	TYR B:133	BINDING SITE FOR RESIDUE BR B 1010
18	BC9	SOFTWARE	THR B:173 , THR B:175	BINDING SITE FOR RESIDUE BR B 1011
19	CC1	SOFTWARE	ARG A:31 , ASN A:33 , SER A:46 , BR A:1009 , GLU B:224 , TRP B:225 , BR B:1005	BINDING SITE FOR MONO-SACCHARIDE NAG A1001 BOUND TO ASN A 33
20	CC2	SOFTWARE	TRP A:225 , BR A:1008 , ARG B:31 , ASN B:33 , SER B:46 , BR B:1007	BINDING SITE FOR MONO-SACCHARIDE NAG B1001 BOUND TO ASN B 33

(no "SS Bond" information available for 3WCR)

Asymmetric Unit

No.	Residues
1	Ala A:106	-	Asp A:107
2	Ala B:106	-	Asp B:107

(no "SAP(SNP)/Variant" information available for 3WCR)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	PHAE_PHAVU	142-148	2	A:142-148 B:142-148
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	PHAE_PHAVU	222-231	2	A:222-231 B:222-231

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	PHAE_PHAVU	142-148	4	A:142-148 B:142-148
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	PHAE_PHAVU	222-231	4	A:222-231 B:222-231

(no "Exon" information available for 3WCR)

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:229
 aligned with PHAE_PHAVU | P05088 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:235
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
           PHAE_PHAVU    22 ASQTSFSFQRFNETNLILQRDATVSSKGQLRLTNVNDNGEPTLSSLGRAFYSAPIQIWDNTTGAVAASPTSFTFNIDVPNNSGPADGLAFVLLPVGSQPKDKGGLLGLFNNYKYDSNAHTVAVEFDTLYNVHWDPKPRHIGIDVNSIKSIKTTTWDFVKGENAEVLITYDSSTKLLVASLVYPSLKTSFIVSDTVDLKSVLPEWVIVGFTATTGITKGNVETNDILSWSFASKLS 256
               SCOP domains d3wcra_ A: automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhh.eeeee..ee.....ee..............eeeeee...ee.ee....ee.eeeeeeeee..........eeeeeeeee.......hhhhh........hhhhh.eeeeee...------...eeeeee......eeee.......eeeeeeeee....eeeeeeee....eeeeeeee.hhhhh...eeeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wcr A  22 ASQTSFSFQRFNETNLILQRDATVSSKGQLRLTNVNDNGEPTLSSLGRAFYSAPIQIWDNTTGAVASFATSFTFNIDVPNNSGPADGLAFVLLPVGSQPKDKGGLLGLFNNYKYDSNAHTVAVEFDTLY------KPRHIGIDVNSIKSIKTTTWDFVKGENAEVLITYDSSTKLLVASLVYPSLKTSFIVSDTVDLKSVLPEWVIVGFTATTGITKGNVETNDILSWSFASKLS 256
                                    31        41        51        61        71        81        91       101       111       121       131       141        |-     | 161       171       181       191       201       211       221       231       241       251     
                                                                                                                                                          150    157

Chain A from PDB  Type:PROTEIN  Length:229
 aligned with V5YN37_PHAVU | V5YN37 from UniProtKB/TrEMBL  Length:275

    Alignment length:235
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
         V5YN37_PHAVU    22 ASQTSFSFQRFNETNLILQRDATVSSKGQLRLTNVNDNGEPTLSSLGRAFYSAPIQIWDNTTGAVASFATSFTFNIDVPNNSGPADGLAFVLLPVGSQPKDKGGLLGLFNNYKYDSNAHTVAVEFDTLYNVHWDPKPRHIGIDVNSIKSIKTTTWDFVKGENAEVLITYDSSTKLLVASLVYPSLKTSFIVSDTVDLKSVLPEWVIVGFTATTGITKGNVETNDILSWSFASKLS 256
               SCOP domains d3wcra_ A: automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhh.eeeee..ee.....ee..............eeeeee...ee.ee....ee.eeeeeeeee..........eeeeeeeee.......hhhhh........hhhhh.eeeeee...------...eeeeee......eeee.......eeeeeeeee....eeeeeeee....eeeeeeee.hhhhh...eeeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wcr A  22 ASQTSFSFQRFNETNLILQRDATVSSKGQLRLTNVNDNGEPTLSSLGRAFYSAPIQIWDNTTGAVASFATSFTFNIDVPNNSGPADGLAFVLLPVGSQPKDKGGLLGLFNNYKYDSNAHTVAVEFDTLY------KPRHIGIDVNSIKSIKTTTWDFVKGENAEVLITYDSSTKLLVASLVYPSLKTSFIVSDTVDLKSVLPEWVIVGFTATTGITKGNVETNDILSWSFASKLS 256
                                    31        41        51        61        71        81        91       101       111       121       131       141        |-     | 161       171       181       191       201       211       221       231       241       251     
                                                                                                                                                          150    157

Chain B from PDB  Type:PROTEIN  Length:235
 aligned with PHAE_PHAVU | P05088 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:249
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261         
           PHAE_PHAVU    22 ASQTSFSFQRFNETNLILQRDATVSSKGQLRLTNVNDNGEPTLSSLGRAFYSAPIQIWDNTTGAVAASPTSFTFNIDVPNNSGPADGLAFVLLPVGSQPKDKGGLLGLFNNYKYDSNAHTVAVEFDTLYNVHWDPKPRHIGIDVNSIKSIKTTTWDFVKGENAEVLITYDSSTKLLVASLVYPSLKTSFIVSDTVDLKSVLPEWVIVGFTATTGITKGNVETNDILSWSFASKLSDGTTSEALNLANFA 270
               SCOP domains d3wcrb_ B: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhh.eeeee..ee.....ee..............eeeeee...ee.ee....ee.eeeeeeeeee.........eeeeeeeee.......hhhhh........hhhhh.eeeeee...------...eeeeee......eeee......eeeeeeeeee....eeeeeee......eeeeeee.hhhhh...eeeeeeeeee..........eeeeeeeeeee.--------.hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG--------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wcr B  22 ASQTSFSFQRFNETNLILQRDATVSSKGQLRLTNVNDNGEPTLSSLGRAFYSAPIQIWDNTTGAVASFATSFTFNIDVPNNSGPADGLAFVLLPVGSQPKDKGGLLGLFNNYKYDSNAHTVAVEFDTLY------KPRHIGIDVNSIKSIKTTTWDFVKGENAEVLITYDSSTKLLVASLVYPSLKTSFIVSDTVDLKSVLPEWVIVGFTATTGITKGNVETNDILSWSFASKLS--------NLANFA 270
                                    31        41        51        61        71        81        91       101       111       121       131       141        |-     | 161       171       181       191       201       211       221       231       241       251    |    -   |     
                                                                                                                                                          150    157                                                                                                256      265

Chain B from PDB  Type:PROTEIN  Length:235
 aligned with V5YN37_PHAVU | V5YN37 from UniProtKB/TrEMBL  Length:275

    Alignment length:249
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261         
         V5YN37_PHAVU    22 ASQTSFSFQRFNETNLILQRDATVSSKGQLRLTNVNDNGEPTLSSLGRAFYSAPIQIWDNTTGAVASFATSFTFNIDVPNNSGPADGLAFVLLPVGSQPKDKGGLLGLFNNYKYDSNAHTVAVEFDTLYNVHWDPKPRHIGIDVNSIKSIKTTTWDFVKGENAEVLITYDSSTKLLVASLVYPSLKTSFIVSDTVDLKSVLPEWVIVGFTATTGITKGNVETNDILSWSFASKLSDGTTSEALNLANFA 270
               SCOP domains d3wcrb_ B: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhh.eeeee..ee.....ee..............eeeeee...ee.ee....ee.eeeeeeeeee.........eeeeeeeee.......hhhhh........hhhhh.eeeeee...------...eeeeee......eeee......eeeeeeeeee....eeeeeee......eeeeeee.hhhhh...eeeeeeeeee..........eeeeeeeeeee.--------.hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wcr B  22 ASQTSFSFQRFNETNLILQRDATVSSKGQLRLTNVNDNGEPTLSSLGRAFYSAPIQIWDNTTGAVASFATSFTFNIDVPNNSGPADGLAFVLLPVGSQPKDKGGLLGLFNNYKYDSNAHTVAVEFDTLY------KPRHIGIDVNSIKSIKTTTWDFVKGENAEVLITYDSSTKLLVASLVYPSLKTSFIVSDTVDLKSVLPEWVIVGFTATTGITKGNVETNDILSWSFASKLS--------NLANFA 270
                                    31        41        51        61        71        81        91       101       111       121       131       141        |-     | 161       171       181       191       201       211       221       231       241       251    |    -   |     
                                                                                                                                                          150    157                                                                                                256      265

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: Legume lectins (238)

Protein domain: automated matches (63)

French bean (Phaseolus vulgaris) [TaxId: 3885] (3)

1a	d3wcra_	A:
1b	d3wcrb_	B:

(no "CATH Domain" information available for 3WCR)

(no "Pfam Domain" information available for 3WCR)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PHAE_PHAVU | P05088)

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:0005537	mannose binding	Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
biological process
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.

Chain A,B (V5YN37_PHAVU | V5YN37)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:106 - Asp A:107	[ RasMol ]
		Ala B:106 - Asp B:107	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	PHAE_PHAVU \| P05088	:	3wcs 3wog 5ava
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 21)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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Related Entries Specified in the PDB File