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Description

Title :   STRUCTURE OF THE LECTIN MPA COMPLEXED WITH T-ANTIGEN DISACCHARIDE

Authors :   X. Lee, A. Thompson, Z. Zhang, T. -T. Hoa, J. Biesterfeldt, C. Ogata, L. X R. A. Z. Johnston, N. M. Young

Date :   05 Dec 97 (Deposition) - 30 Dec 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)

Keywords :   Multi-Wavelength Anomalous Diffraction (Mad), T-Antigen, Lectin, Maclura Pomifera, Beta Prism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Lee, A. Thompson, Z. Zhang, H. Ton-That, J. Biesterfeldt, C. Ogata, L. Xu, R. A. Johnston, N. M. Young
Structure Of The Complex Of Maclura Pomifera Agglutinin And The T-Antigen Disaccharide, Galbeta1, 3Galnac.
J. Biol. Chem. V. 273 6312 1998
PubMed-ID: 9497359 | Reference-DOI: 10.1074/JBC.273.11.6312

Compounds

Molecule 1 - AGGLUTININ
	Chains	:	A
	Organ	:	SEEDS
	Organism Common	:	OSAGE ORANGE
	Organism Scientific	:	MACLURA POMIFERA
	Organism Taxid	:	3496
	Other Details	:	FROM THE SEEDS OF THE MORACEAE PLANT FAMILY

Molecule 2 - AGGLUTININ
	Chains	:	B
	Organ	:	SEEDS
	Organism Common	:	OSAGE ORANGE
	Organism Scientific	:	MACLURA POMIFERA
	Organism Taxid	:	3496
	Other Details	:	FROM THE SEEDS OF THE MORACEAE PLANT FAMILY

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	A2G	1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	GAL	1	Ligand/Ion	BETA-D-GALACTOSE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	A2G	4	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	GAL	4	Ligand/Ion	BETA-D-GALACTOSE

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:76 , GLY A:77 , TYR A:78 , A2G A:135 , HOH A:171 , HOH A:189	BINDING SITE FOR RESIDUE GAL A 134
2	AC2	SOFTWARE	GLY A:1 , PHE A:47 , TYR A:78 , TYR A:122 , TRP A:123 , ASP A:125 , GAL A:134	BINDING SITE FOR RESIDUE A2G A 135

SS Bonds (0, 0)

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

Cis Peptide Bonds (3, 3)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 7)

Asymmetric Unit (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LECA_MACPO_001 *	T	31	V	LECA_MACPO	---	---	A	T	31	V
2	UniProt	VAR_LECA_MACPO_002 *	K	52	T	LECA_MACPO	---	---	A	K	52	T
3	UniProt	VAR_LECA_MACPO_003 *	E	59	D	LECA_MACPO	---	---	A	E	59	D
4	UniProt	VAR_LECA_MACPO_004 *	V	72	I	LECA_MACPO	---	---	A	V	72	I
5	UniProt	VAR_LECA_MACPO_005 *	I	81	V	LECA_MACPO	---	---	A	I	81	V
6	UniProt	VAR_LECA_MACPO_006 *	N	110	Q	LECA_MACPO	---	---	A	N	110	Q
7	UniProt	VAR_LECA_MACPO_007 *	L	112	G	LECA_MACPO	---	---	A	L	112	G
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (7, 28)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LECA_MACPO_001 *	T	31	V	LECA_MACPO	---	---	A	T	31	V
2	UniProt	VAR_LECA_MACPO_002 *	K	52	T	LECA_MACPO	---	---	A	K	52	T
3	UniProt	VAR_LECA_MACPO_003 *	E	59	D	LECA_MACPO	---	---	A	E	59	D
4	UniProt	VAR_LECA_MACPO_004 *	V	72	I	LECA_MACPO	---	---	A	V	72	I
5	UniProt	VAR_LECA_MACPO_005 *	I	81	V	LECA_MACPO	---	---	A	I	81	V
6	UniProt	VAR_LECA_MACPO_006 *	N	110	Q	LECA_MACPO	---	---	A	N	110	Q
7	UniProt	VAR_LECA_MACPO_007 *	L	112	G	LECA_MACPO	---	---	A	L	112	G
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JACALIN_LECTIN	PS51752	Jacalin-type lectin domain profile.	LECA_MACPO	1-133	1	A:1-133

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JACALIN_LECTIN	PS51752	Jacalin-type lectin domain profile.	LECA_MACPO	1-133	4	A:1-133

Exons (0, 0)

(no "Exon" information available for 1JOT)

Sequences/Alignments

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:133
 aligned with LECA_MACPO | P18674 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   
           LECA_MACPO     1 GVTFDDGAYTGIREINFEYNSETAIGGLRVTYDLNGMPFVAEDHKSFITGFKPVKISLEFPSEYIVEVSGYVGKVEGYTVIRSLTFKTNKQTYGPYGVTNGTPFSLPIENGLIVGFKGSIGYWLDYFSIYLSL 133
               SCOP domains d1jot.2 B:,A: Lectin MPA                                                                                                              SCOP domains
               CATH domains 1jotA00 A:1-133  [code=2.100.10.30, no name defined]                                                                                  CATH domains
               Pfam domains Jacalin-1jotA01 A:1-133                                                                                                               Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee........eeeeeee..eeee...........eeeeee.......eeeeeeeeeee..eeee.eeeeee.............eeeeee....eeeeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------V--------------------T------D------------I--------V----------------------------Q-G--------------------- SAPs(SNPs)
                    PROSITE JACALIN_LECTIN  PDB: A:1-133 UniProt: 1-133                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jot A   1 GVTFDDGAYTGIREINFEYNSETAIGGLRVTYDLNGMPFVAEDHKSFITGFKPVKISLEFPSEYIVEVSGYVGKVEGYTVIRSLTFKTNKQTYGPYGVTNGTPFSLPIENGLIVGFKGSIGYWLDYFSIYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:16
 aligned with LECB2_MACPO | P18676 from UniProtKB/Swiss-Prot  Length:20

    Alignment length:16
                                    11      
          LECB2_MACPO     2 RNGKSQSIIVGPWGDR  17
               SCOP domains d1jot.2 B:,A:    SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ................ Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 1jot B   3 RNGKSQSIIVGPWGDR  18
                                    12

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-Prism I (50)

Superfamily: Mannose-binding lectins (42)

Family: Mannose-binding lectins (32)

Protein domain: Lectin MPA (1)

Osage orange (Maclura pomifera) [TaxId: 3496] (1)

d1jot.2

B:,A:

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Aligned Prism (39)

Topology: Vitelline Membrane Outer Layer Protein I, subunit A (39)

Homologous Superfamily: [code=2.100.10.30, no name defined] (33)

Osage orange (Maclura pomifera) (1)

1jotA00

A:1-133

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Jacalin] (35)

Family: Jacalin (35)

Maclura pomifera (Osage orange) (Ioxylon pomiferum) (4)

Jacalin-1jotA01

A:1-133

Gene Ontology (1, 2)

Asymmetric Unit(hide GO term definitions)

Chain A (LECA_MACPO | P18674)

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.

Chain B (LECB2_MACPO | P18676)

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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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	LECA_MACPO \| P18674	:	3lly 3llz 3lm1
	LECB2_MACPO \| P18676	:	3lly 3llz 3lm1

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