3LLY - JenaLib

Title :   CRYSTAL STRUCTURE ANALYSIS OF MACLURA POMIFERA AGGLUTININ

Authors :   J. Huang, Z. Xu, D. Wang, C. Ogato, T. Hirama, K. Palczewski, S. L. Hazen, N. M. Young

Date :   29 Jan 10 (Deposition) - 22 Sep 10 (Release) - 22 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)
Biol. Unit 2: A,B  (1x)

Keywords :   Maclura Pomifera Agglutinin, Mpa, Lectin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Huang, Z. Xu, D. Wang, C. M. Ogata, K. Palczewski, X. Lee, N. M. Young
Characterization Of The Secondary Binding Sites Of Maclura Pomifera Agglutinin By Glycan Array And Crystallographic Analyses.
Glycobiology V. 20 1643 2010
PubMed-ID: 20826825 | Reference-DOI: 10.1093/GLYCOB/CWQ118

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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)

Biological Unit 2 (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)

PROSITE Motifs (1, 1)

Exons (0, 0)

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 ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Jacalin-3llyA01 A:1-133                                                                                                               Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeee....eeeeeeeee...eeeeeeeee. 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
                 3lly 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
                                    10      
          LECB2_MACPO     1 GRNGKSQSIIVGPWGD  16
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 3lly B   2 GRNGKSQSIIVGPWGD  17
                                    11

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

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.

Visualization

Interactive Views

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
(no "Ligands, Modified Residues, Ions" information available for 3lly)

	Sites
(no "Sites" information available for 3lly)

	Cis Peptide Bonds
		Gly A:94 - Pro A:95	[ RasMol ]
		Gly B:13 - Pro B:14	[ RasMol ]
		Phe A:60 - Pro A:61	[ RasMol ]

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

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3lly
		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
	LECA_MACPO \| P18674
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	LECB2_MACPO \| P18676
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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

Analysis Tools

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
	LECA_MACPO \| P18674
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	LECB2_MACPO \| P18676
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description