2ZQO - JenaLib

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

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 :   1.80

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, 9)

No.	Name	Count	Type	Full Name
1	CD	1	Ligand/Ion	CADMIUM ION
2	IMD	1	Ligand/Ion	IMIDAZOLE
3	NGA	4	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
4	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	IMD	1	Ligand/Ion	IMIDAZOLE
3	NGA	2	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	IMD	-1	Ligand/Ion	IMIDAZOLE
3	NGA	2	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	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 , HOH A:475 , HOH A:484 , HOH A:604 , THR B:168 , HOH B:448	BINDING SITE FOR RESIDUE NGA A 270
2	AC2	SOFTWARE	SER A:138 , GLU A:139 , GLY A:142 , ASP A:230 , ILE A:231 , ILE A:232 , LYS A:233 , HIS A:248 , ASN A:252 , HOH A:462 , HOH A:498 , HOH A:530 , HOH A:544 , HOH A:547 , HOH A:612	BINDING SITE FOR RESIDUE NGA A 271
3	AC3	SOFTWARE	HIS A:241 , IMD A:451 , HOH A:555 , HOH A:557 , HIS B:241 , HOH B:516	BINDING SITE FOR RESIDUE CD A 401
4	AC4	SOFTWARE	ASN A:217 , LYS A:233 , LYS A:254 , HOH A:566 , HOH A:595	BINDING SITE FOR RESIDUE PO4 A 421
5	AC5	SOFTWARE	GLY A:239 , HIS A:241 , CD A:401 , GLY B:239 , HIS B:241	BINDING SITE FOR RESIDUE IMD A 451
6	AC6	SOFTWARE	THR A:168 , HOH A:508 , ASP B:146 , ILE B:147 , GLU B:148 , GLY B:149 , GLN B:150 , TRP B:161 , LYS B:164 , ASN B:171 , HOH B:450 , HOH B:476 , HOH B:557	BINDING SITE FOR RESIDUE NGA B 301
7	AC7	SOFTWARE	SER B:138 , GLU B:139 , GLY B:142 , ASP B:230 , ILE B:231 , ILE B:232 , LYS B:233 , HIS B:248 , ASN B:252 , HOH B:443 , HOH B:449 , HOH B:468 , HOH B:485 , HOH B:526	BINDING SITE FOR RESIDUE NGA B 302
8	AC8	SOFTWARE	ASN B:217 , LYS B:233 , LYS B:254	BINDING SITE FOR RESIDUE PO4 B 422
9	AC9	SOFTWARE	LYS B:143 , HOH B:504 , HOH B:538 , HOH B:564	BINDING SITE FOR RESIDUE PO4 B 423

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

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

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

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

(no "Exon" information available for 2ZQO)

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:130
 aligned with O96048_LUMTE | O96048 from UniProtKB/TrEMBL  Length:260

    Alignment length:130
                                   140       150       160       170       180       190       200       210       220       230       240       250       260
         O96048_LUMTE   131 PKFFYIKSELNGKVLDIEGQNPAPGSKIITWDQKKGPTAVNQLWYTDQQGVIRSKLNDFAIDASHEQIETQPFDPNNPKRAWIVSGNTIAQLSDRDIVLDIIKSDKEAGAHICAWKQHGGPNQKFIIESE 260
               SCOP domains d2zqoa1 A:131-260 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
                 2zqo A 131 PKFFYIKSELNGKVLDIEGQNPAPGSKIITWDQKKGPTAVNQLWYTDQQGVIRSKLNDFAIDASHEQIETQPFDPNNPKRAWIVSGNTIAQLSDRDIVLDIIKSDKEAGAHICAWKQHGGPNQKFIIESE 260
                                   140       150       160       170       180       190       200       210       220       230       240       250       260

Chain B from PDB  Type:PROTEIN  Length:130
 aligned with O96048_LUMTE | O96048 from UniProtKB/TrEMBL  Length:260

    Alignment length:130
                                   140       150       160       170       180       190       200       210       220       230       240       250       260
         O96048_LUMTE   131 PKFFYIKSELNGKVLDIEGQNPAPGSKIITWDQKKGPTAVNQLWYTDQQGVIRSKLNDFAIDASHEQIETQPFDPNNPKRAWIVSGNTIAQLSDRDIVLDIIKSDKEAGAHICAWKQHGGPNQKFIIESE 260
               SCOP domains d2zqob_ B: 29-kDa galactose-binding lectin                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Ricin_B_lectin-2zqoB01 B:131-255                                                                                             ----- Pfam domains (1)
           Pfam domains (2) Ricin_B_lectin-2zqoB02 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
                 2zqo B 131 PKFFYIKSELNGKVLDIEGQNPAPGSKIITWDQKKGPTAVNQLWYTDQQGVIRSKLNDFAIDASHEQIETQPFDPNNPKRAWIVSGNTIAQLSDRDIVLDIIKSDKEAGAHICAWKQHGGPNQKFIIESE 260
                                   140       150       160       170       180       190       200       210       220       230       240       250       260

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	d2zqoa1	A:131-260
1b	d2zqob_	B:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Trefoil (131)

Family: Ricin_B_lectin (25)

Lumbricus terrestris (Common earthworm) (2)

1a	Ricin_B_lectin-2zqoB01	B:131-255
1b	Ricin_B_lectin-2zqoB02	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.

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

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

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.
2zqn

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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