2ZQN - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE EARTHWORM R-TYPE LECTIN C-HALF IN COMPLEX WITH LACTOSE

Authors :   R. Suzuki, A. Kuno, T. Hasegawa, J. Hirabayashi, K. Kasai, M. Momma, Z. Fujimoto

Date :   13 Aug 08 (Deposition) - 02 Sep 08 (Release) - 10 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Earthworm Lumbricus Terrestris, Hemagglutinin, R-Type Lectin, Beta-Trefoil Fold, Sugar Complex, Lectin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Suzuki, A. Kuno, T. Hasegawa, J. Hirabayashi, K. Kasai, M. Momma, Z. Fujimoto
Sugar-Complex Structures Of The C-Half Domain Of The Galactose-Binding Lectin Ew29 From The Earthworm Lumbricus Terrestris
Acta Crystallogr. , Sect. D V. 65 49 2009
PubMed-ID: 19153466 | Reference-DOI: 10.1107/S0907444908037451
(for further references see the PDB file header)

Molecule 1 - 29-KDA GALACTOSE-BINDING LECTIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN
	Organism Common	:	COMMON EARTHWORM
	Organism Scientific	:	LUMBRICUS TERRESTRIS
	Organism Taxid	:	6398

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 12)

No.	Name	Count	Type	Full Name
1	BGC	4	Ligand/Ion	BETA-D-GLUCOSE
2	GAL	4	Ligand/Ion	BETA-D-GALACTOSE
3	IMD	2	Ligand/Ion	IMIDAZOLE
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
2	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
3	IMD	2	Ligand/Ion	IMIDAZOLE
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
2	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
3	IMD	-1	Ligand/Ion	IMIDAZOLE
4	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:149 , GLU A:237 , GAL A:302 , PO4 A:401 , HOH A:471 , HOH A:537 , LYS B:130 , GLN B:178	BINDING SITE FOR RESIDUE BGC A 301
02	AC2	SOFTWARE	ASP A:146 , ILE A:147 , GLU A:148 , GLY A:149 , GLN A:150 , TRP A:161 , LYS A:164 , ASN A:171 , BGC A:301 , PO4 A:401 , HOH A:455	BINDING SITE FOR RESIDUE GAL A 302
03	AC3	SOFTWARE	LYS A:233 , GAL A:312 , PO4 A:402 , HOH A:475 , HOH A:530	BINDING SITE FOR RESIDUE BGC A 311
04	AC4	SOFTWARE	ASP A:230 , ILE A:232 , LYS A:233 , TRP A:245 , HIS A:248 , ASN A:252 , BGC A:311 , HOH A:550	BINDING SITE FOR RESIDUE GAL A 312
05	AC5	SOFTWARE	TRP A:161 , LYS A:164 , BGC A:301 , GAL A:302 , HOH A:469 , HOH A:496 , HOH A:505 , HOH A:516	BINDING SITE FOR RESIDUE PO4 A 401
06	AC6	SOFTWARE	LEU A:222 , BGC A:311 , IMD A:421 , HOH A:506 , HOH A:538 , LYS B:185 , HOH B:418	BINDING SITE FOR RESIDUE PO4 A 402
07	AC7	SOFTWARE	GLN A:179 , GLY A:180 , ILE A:213 , LEU A:222 , ARG A:225 , PO4 A:402 , LYS B:185 , LEU B:186 , HOH B:342	BINDING SITE FOR RESIDUE IMD A 421
08	AC8	SOFTWARE	LYS A:185 , LEU A:186 , HOH A:430 , GLN B:179 , ILE B:213 , LEU B:222 , ARG B:225	BINDING SITE FOR RESIDUE IMD A 422
09	AC9	SOFTWARE	LYS A:130 , GLN A:178 , GLY B:149 , GAL B:322 , HOH B:458	BINDING SITE FOR RESIDUE BGC B 321
10	BC1	SOFTWARE	ASP B:146 , ILE B:147 , GLU B:148 , GLY B:149 , GLN B:150 , TRP B:161 , LYS B:164 , ASN B:171 , BGC B:321 , HOH B:391 , HOH B:446	BINDING SITE FOR RESIDUE GAL B 322
11	BC2	SOFTWARE	LYS B:233 , HIS B:248 , GLY B:250 , GAL B:332 , HOH B:363 , HOH B:382 , HOH B:423	BINDING SITE FOR RESIDUE BGC B 331
12	BC3	SOFTWARE	ASP B:230 , ILE B:231 , ILE B:232 , LYS B:233 , TRP B:245 , HIS B:248 , ASN B:252 , BGC B:331 , HOH B:379 , HOH B:398 , HOH B:437	BINDING SITE FOR RESIDUE GAL B 332

(no "SS Bond" information available for 2ZQN)

(no "Cis Peptide Bond" information available for 2ZQN)

(no "SAP(SNP)/Variant" information available for 2ZQN)

(no "PROSITE Motif" information available for 2ZQN)

(no "Exon" information available for 2ZQN)

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:131
 aligned with O96048_LUMTE | O96048 from UniProtKB/TrEMBL  Length:260

    Alignment length:131
                                   139       149       159       169       179       189       199       209       219       229       239       249       259 
         O96048_LUMTE   130 KPKFFYIKSELNGKVLDIEGQNPAPGSKIITWDQKKGPTAVNQLWYTDQQGVIRSKLNDFAIDASHEQIETQPFDPNNPKRAWIVSGNTIAQLSDRDIVLDIIKSDKEAGAHICAWKQHGGPNQKFIIESE 260
               SCOP domains d2zqna_ A: 29-kDa galactose-binding lectin                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....eeee.hhh......eeee....hhhhhhh.eee.....eee.....eee......eee.....hhhh.eeee..eeee..eeeeeeee.hhh......eeeee...hhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zqn A 130 KPKFFYIKSELNGKVLDIEGQNPAPGSKIITWDQKKGPTAVNQLWYTDQQGVIRSKLNDFAIDASHEQIETQPFDPNNPKRAWIVSGNTIAQLSDRDIVLDIIKSDKEAGAHICAWKQHGGPNQKFIIESE 260
                                   139       149       159       169       179       189       199       209       219       229       239       249       259

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with O96048_LUMTE | O96048 from UniProtKB/TrEMBL  Length:260

    Alignment length:131
                                   139       149       159       169       179       189       199       209       219       229       239       249       259 
         O96048_LUMTE   130 KPKFFYIKSELNGKVLDIEGQNPAPGSKIITWDQKKGPTAVNQLWYTDQQGVIRSKLNDFAIDASHEQIETQPFDPNNPKRAWIVSGNTIAQLSDRDIVLDIIKSDKEAGAHICAWKQHGGPNQKFIIESE 260
               SCOP domains d2zqnb_ B: 29-kDa galactose-binding lectin                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Ricin_B_lectin-2zqnB01 B:131-255                                                                                             ----- Pfam domains (1)
           Pfam domains (2) -Ricin_B_lectin-2zqnB02 B:131-255                                                                                             ----- Pfam domains (2)
         Sec.struct. author ....eeeee.....eeee.hhh......eeee....hhhhhhh.eee.....eee.....eee......eee.....hhhh.eeee..eeee..eeeeeeee.hhh......eeeee...hhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zqn B 130 KPKFFYIKSELNGKVLDIEGQNPAPGSKIITWDQKKGPTAVNQLWYTDQQGVIRSKLNDFAIDASHEQIETQPFDPNNPKRAWIVSGNTIAQLSDRDIVLDIIKSDKEAGAHICAWKQHGGPNQKFIIESE 260
                                   139       149       159       169       179       189       199       209       219       229       239       249       259

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: beta-Trefoil (385)

Superfamily: Ricin B-like lectins (91)

Family: Ricin B-like (65)

Protein domain: 29-kDa galactose-binding lectin (3)

Common earthworm (Lumbricus terrestris) [TaxId: 6398] (3)

1a	d2zqna_	A:
1b	d2zqnb_	B:

(no "CATH Domain" information available for 2ZQN)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Trefoil (131)

Family: Ricin_B_lectin (25)

Lumbricus terrestris (Common earthworm) (2)

1a	Ricin_B_lectin-2zqnB01	B:131-255
1b	Ricin_B_lectin-2zqnB02	B:131-255

Asymmetric Unit(hide GO term definitions)

Chain A,B (O96048_LUMTE | O96048)

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BGC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		IMD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2zqn)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2zqn
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	O96048_LUMTE \| O96048
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	O96048_LUMTE \| O96048
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	O96048_LUMTE \| O96048	:	2dry 2drz 2ds0 2rst 2zqo

2dry	LIGAND FREE FORM OF THE MUTANT LECTIN.
2drz	THE MUTANT LECTIN IN COMPLEX WITH LACTOSE.
2ds0	THE MUTANT LECTIN IN COMPLEX WITH 6'-SIALYLLACTOSE.
2zqo

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (1, 1)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File