1DGL - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   LECTIN FROM DIOCLEA GRANDIFLORA COMPLEXED TO TRIMANNOSIDE

Authors :   D. A. Rozwarski, B. M. Swami, C. F. Brewer, J. C. Sacchettini

Date :   10 Feb 98 (Deposition) - 01 Jun 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Lectin, Saccharide Binding, Trimannoside (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. A. Rozwarski, B. M. Swami, C. F. Brewer, J. C. Sacchettini
Crystal Structure Of The Lectin From Dioclea Grandiflora Complexed With Core Trimannoside Of Asparagine-Linked Carbohydrates.
J. Biol. Chem. V. 273 32818 1998
PubMed-ID: 9830028 | Reference-DOI: 10.1074/JBC.273.49.32818
(for further references see the PDB file header)

Molecule 1 - LECTIN
	Chains	:	A, B
	Organism Common	:	MUCANA
	Organism Scientific	:	DIOCLEA GRANDIFLORA
	Organism Taxid	:	3837
	Other Details	:	TRIMANNOSIDE COMPLEX

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
3	MMA	2	Ligand/Ion	O1-METHYL-MANNOSE
4	MN	2	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MAN	8	Ligand/Ion	ALPHA-D-MANNOSE
3	MMA	4	Ligand/Ion	O1-METHYL-MANNOSE
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:12 , ASN A:14 , GLY A:98 , LEU A:99 , TYR A:100 , ALA A:207 , ASP A:208 , GLY A:227 , ARG A:228 , MMA A:401 , HOH A:560 , HOH A:586	BINDING SITE FOR RESIDUE MAN A 400
02	AC2	SOFTWARE	TYR A:12 , MAN A:400 , MAN A:402 , HOH A:539 , HOH A:541	BINDING SITE FOR RESIDUE MMA A 401
03	AC3	SOFTWARE	TYR A:12 , PRO A:13 , ASN A:14 , THR A:15 , ASP A:16 , MMA A:401 , HOH A:567	BINDING SITE FOR RESIDUE MAN A 402
04	AC4	SOFTWARE	TYR B:12 , ASN B:14 , GLY B:98 , LEU B:99 , TYR B:100 , ALA B:207 , ASP B:208 , GLY B:227 , ARG B:228 , MMA B:401 , HOH B:560 , HOH B:566 , HOH B:587	BINDING SITE FOR RESIDUE MAN B 400
05	AC5	SOFTWARE	TYR B:12 , MAN B:400 , MAN B:402 , HOH B:539 , HOH B:541 , HOH B:585 , HOH B:604	BINDING SITE FOR RESIDUE MMA B 401
06	AC6	SOFTWARE	HOH A:527 , HOH A:573 , TYR B:12 , PRO B:13 , ASN B:14 , THR B:15 , ASP B:16 , MMA B:401	BINDING SITE FOR RESIDUE MAN B 402
07	AC7	SOFTWARE	ASN A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:501 , HOH A:502	BINDING SITE FOR RESIDUE CA A 301
08	AC8	SOFTWARE	GLU A:8 , ASN A:10 , ASP A:19 , HIS A:24 , HOH A:503 , HOH A:504	BINDING SITE FOR RESIDUE MN A 302
09	AC9	SOFTWARE	ASN B:10 , TYR B:12 , ASN B:14 , ASP B:19 , HOH B:501 , HOH B:502	BINDING SITE FOR RESIDUE CA B 301
10	BC1	SOFTWARE	GLU B:8 , ASN B:10 , ASP B:19 , HIS B:24 , HOH B:503 , HOH B:504	BINDING SITE FOR RESIDUE MN B 302

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

Asymmetric Unit

No.	Residues
1	Ala A:207	-	Asp A:208
2	Ala B:207	-	Asp B:208

(no "SAP(SNP)/Variant" information available for 1DGL)

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.	LECA_DIOGR	5-11	2	A:5-11 B:5-11
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LECA_DIOGR	85-94	2	A:85-94 B:85-94

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.	LECA_DIOGR	5-11	4	A:5-11 B:5-11
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LECA_DIOGR	85-94	4	A:85-94 B:85-94

(no "Exon" information available for 1DGL)

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:237
 aligned with LECA_DIOGR | P08902 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
           LECA_DIOGR     1 ADTIVAVELDSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYSGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADENSLHFSFHKFSQNPKDLILQGDAFTDSDGNLELTKVSSSGDPQGNSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDREPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 237
               SCOP domains d1dgla_ A: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1dglA00 A:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhh......eeeeee......eeee.......eeeeeeeee....eeeeeeee.....eeeeee..hhhh....eeeeeeee........eeeeeeeeeeee.......eeeeeee.........eeeee.........................eeeeee............eeeeeeeeeee..........eeeeeeee..........hhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dgl A   1 ADTIVAVELNSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYSGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANSLHFSFHQFSQNPKDLILQGDAFTDSDGNLELTKVSSSGDPQGNSVGRALFYAPVHIWEKSAVVASFDATFTFLIKSPDREPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:237
 aligned with LECA_DIOGR | P08902 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
           LECA_DIOGR     1 ADTIVAVELDSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYSGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADENSLHFSFHKFSQNPKDLILQGDAFTDSDGNLELTKVSSSGDPQGNSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDREPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 237
               SCOP domains d1dglb_ B: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1dglB00 B:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhh......eeeeee......eeee.......eeeeeeeee....eeeeeeee.....eeeeee..hhhh....eeeeeeee........eeeeeeeeeee........eeeeeee.........eeeee.........................eeeeee.............eeeeeeeeee..........eeeeeeee..........hhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dgl B   1 ADTIVAVELNSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYSGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANSLHFSFHQFSQNPKDLILQGDAFTDSDGNLELTKVSSSGDPQGNSVGRALFYAPVHIWEKSAVVASFDATFTFLIKSPDREPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

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: Legume lectin (110)

Mucana (Dioclea grandiflora) [TaxId: 3837] (1)

1a	d1dgla_	A:
1b	d1dglb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.200, no name defined] (421)

Mucana (Dioclea grandiflora) (1)

1a	1dglA00	A:1-237
1b	1dglB00	B:1-237

(no "Pfam Domain" information available for 1DGL)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LECA_DIOGR | P08902)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MAN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MMA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ 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 ]

	Cis Peptide Bonds
		Ala A:207 - Asp A:208	[ RasMol ]
		Ala B:207 - Asp B:208	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	1dgl
		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_DIOGR \| P08902
		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

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_DIOGR \| P08902
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	LECA_DIOGR \| P08902	:	1vln 2gdf 2je9 2jec 4z8b

(no "Related Entries Specified in the PDB File" available for 1DGL)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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