3A07 - 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 ACTINOHIVIN; POTENT ANTI-HIV PROTEIN

Authors :   M. Tsunoda, K. Suzuki, T. Sagara, A. Takenaka

Date :   04 Mar 09 (Deposition) - 25 Aug 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.19

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

Keywords :   Carbohydrate-Binding Module Family 13, Antiviral Protein, Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Tanaka, H. Chiba, J. Inokoshi, A. Kuno, T. Sugai, A. Takahashi, Y. Ito, M. Tsunoda, K. Suzuki, A. Takenaka, T. Sekiguchi, H. Umeyama, J. Hirabayashi, S. Omura
Mechanism By Which The Lectin Actinohivin Blocks Hiv Infection Of Target Cells
Proc. Natl. Acad. Sci. Usa V. 106 15633 2009
PubMed-ID: 19717426 | Reference-DOI: 10.1073/PNAS.0907572106

Molecule 1 - ACTINOHIVIN
	Chains	:	A, B
	Fragment	:	UNP RESIDUES 43-160
	Organism Common	:	LONGISPORA ALBIDA
	Organism Scientific	:	ACTINOMYCETE
	Organism Taxid	:	237531
	Strain	:	K97-0003

		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 (1, 6)

No.	Name	Count	Type	Full Name
1	NA	6	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:126 , ILE A:127 , VAL A:135 , LEU A:136 , GLN A:155 , TRP A:157	BINDING SITE FOR RESIDUE NA A 1
2	AC2	SOFTWARE	THR A:50 , ILE A:51 , LEU A:59 , LEU A:60 , GLN A:79 , TRP A:81	BINDING SITE FOR RESIDUE NA A 2
3	AC3	SOFTWARE	THR A:88 , VAL A:89 , CYS A:97 , LEU A:98 , GLN A:117	BINDING SITE FOR RESIDUE NA A 3
4	AC4	SOFTWARE	THR B:88 , VAL B:89 , CYS B:97 , LEU B:98 , GLN B:117	BINDING SITE FOR RESIDUE NA B 4
5	AC5	SOFTWARE	TYR B:126 , ILE B:127 , VAL B:135 , LEU B:136 , GLN B:155 , TRP B:157	BINDING SITE FOR RESIDUE NA B 5
6	AC6	SOFTWARE	THR B:50 , ILE B:51 , LEU B:59 , LEU B:60 , GLN B:79 , TRP B:81	BINDING SITE FOR RESIDUE NA B 6

Asymmetric Unit

No.	Residues
1	A:97	-	A:111
2	B:97	-	B:111

(no "Cis Peptide Bond" information available for 3A07)

(no "SAP(SNP)/Variant" information available for 3A07)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	AHV_ACTSK	45-160	2	A:45-160 B:45-160

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	AHV_ACTSK	45-160	1	A:45-160 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	AHV_ACTSK	45-160	1	- B:45-160

(no "Exon" information available for 3A07)

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:116
 aligned with AHV_ACTSK | Q9KWN0 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:116
                                    54        64        74        84        94       104       114       124       134       144       154      
            AHV_ACTSK    45 QFASVTIRNAQTGRLLDSNYNGNVYTLPANGGNYQRWTGPGDGTVRNAQTGRCLDSNYDGAVYTLPCNGGSYQKWLFYSNGYIQNVETGRVLDSNYNGNVYTLPANGGNYQKWYTG 160
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.eee.....eeee.....eeee....hhhh.eee......ee.....eeee.....eeee....hhhh.eee.....eee.....eeee.....eeee....hhhh.eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RICIN_B_LECTIN  PDB: A:45-160 UniProt: 45-160                                                                        PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3a07 A  45 QFASVTIRNAQTGRLLDSNYNGNVYTLPANGGNYQRWTGPGDGTVRNAQTGRCLDSNYDGAVYTLPCNGGSYQKWLFYSNGYIQNVETGRVLDSNYNGNVYTLPANGGNYQKWYTG 160
                                    54        64        74        84        94       104       114       124       134       144       154

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with AHV_ACTSK | Q9KWN0 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:118
                                    52        62        72        82        92       102       112       122       132       142       152        
            AHV_ACTSK    43 SAQFASVTIRNAQTGRLLDSNYNGNVYTLPANGGNYQRWTGPGDGTVRNAQTGRCLDSNYDGAVYTLPCNGGSYQKWLFYSNGYIQNVETGRVLDSNYNGNVYTLPANGGNYQKWYTG 160
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.eee.....eeee.....eeee....hhhh.eee......ee.....eeee.....eeee....hhhh.eee.....eee.....eeee.....eeee....hhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RICIN_B_LECTIN  PDB: B:45-160 UniProt: 45-160                                                                        PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3a07 B  43 SAQFASVTIRNAQTGRLLDSNYNGNVYTLPANGGNYQRWTGPGDGTVRNAQTGRCLDSNYDGAVYTLPCNGGSYQKWLFYSNGYIQNVETGRVLDSNYNGNVYTLPANGGNYQKWYTG 160
                                    52        62        72        82        92       102       112       122       132       142       152

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 '\|'

(no "SCOP Domain" information available for 3A07)

(no "CATH Domain" information available for 3A07)

(no "Pfam Domain" information available for 3A07)

Asymmetric Unit(hide GO term definitions)

Chain A,B (AHV_ACTSK | Q9KWN0)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0050688	regulation of defense response to virus	Any process that modulates the frequency, rate or extent of the antiviral response of a cell or organism.

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
		NA	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3a07)

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
	3a07
		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
	AHV_ACTSK \| Q9KWN0
		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
	AHV_ACTSK \| Q9KWN0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	AHV_ACTSK \| Q9KWN0	:	4den 4end 4g1r 4p6a

(no "Related Entries Specified in the PDB File" available for 3A07)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

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