4HQN - 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 MANGANESE-LOADED PLASMODIUM VIVAX TRAP PROTEIN

Authors :   G. Song, A. C. Koksal, C. Lu, T. A. Springer

Date :   25 Oct 12 (Deposition) - 26 Dec 12 (Release) - 09 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Malaria, Sporozoite Motility, Vwa Domain, Tsr Domain, Extensible Beta-Ribbon, Receptor On Sporozoite, Vaccine Target, Sporozoite Surface, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Song, A. C. Koksal, C. Lu, T. A. Springer
Shape Change In The Receptor For Gliding Motility In Plasmodium Sporozoites.
Proc. Natl. Acad. Sci. Usa V. 109 21420 2012
PubMed-ID: 23236185 | Reference-DOI: 10.1073/PNAS.1218581109

Molecule 1 - SPOROZOITE SURFACE PROTEIN 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293T
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Fragment	:	ADHESIVE DOMAINS (UNP RESIDUES 25-283)
	Gene	:	SSP2
	Mutation	:	YES
	Organism Scientific	:	PLASMODIUM VIVAX
	Organism Taxid	:	5855
	Strain	:	SAL I
	Synonym	:	THROMBOSPONDIN REPEAT ANONYMOUS PROTEIN, TRAP

		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, 8)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
4	MN	2	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:52 , SER A:54 , THR A:127 , HOH A:401 , HOH A:402 , HOH A:403	BINDING SITE FOR RESIDUE MN A 301
2	AC2	SOFTWARE	THR A:127 , MET A:129 , THR A:130 , ASN A:162 , SER A:163	BINDING SITE FOR RESIDUE CL A 304
3	AC3	SOFTWARE	SER B:52 , SER B:54 , THR B:127 , HOH B:401 , HOH B:402 , HOH B:403	BINDING SITE FOR RESIDUE MN B 301
4	AC4	SOFTWARE	THR B:127 , MET B:129 , THR B:130 , ASN B:162 , SER B:163	BINDING SITE FOR RESIDUE CL B 304
5	AC5	SOFTWARE	VAL A:251 , THR A:252 , CYS A:253 , HOH A:420 , HOH A:541 , HOH A:662 , HOH A:667 , HOH B:468	BINDING SITE FOR LINKED RESIDUES A 302 to 303
6	AC6	SOFTWARE	ARG A:79 , GLY A:100 , ILE B:61 , VAL B:251 , THR B:252 , HOH B:405 , HOH B:409 , HOH B:445 , HOH B:542 , HOH B:632	BINDING SITE FOR LINKED RESIDUES B 302 to 303

Asymmetric Unit

No.	Residues
1	A:39	-	A:231
2	A:201	-	A:208
3	A:240	-	A:269
4	A:249	-	A:277
5	A:253	-	A:282
6	B:39	-	B:231
7	B:201	-	B:208
8	B:240	-	B:269
9	B:249	-	B:277
10	B:253	-	B:282

(no "Cis Peptide Bond" information available for 4HQN)

(no "SAP(SNP)/Variant" information available for 4HQN)

(no "PROSITE Motif" information available for 4HQN)

(no "Exon" information available for 4HQN)

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:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeeeeee...eeeee...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh......eeeeeeee.....hhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhh..........ee..hhhhhhhhhhhhhh..eeeeeeeee...............eeeeeee..........eeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hqn A  30 DEVKYSEEVCNEQVDLYLLVDGSGSIGYPNWITKVIPMLNGLINSLSLSRDTINLYMNLFGSYTTELIRLGSGQSIDKRQALSKVTELRKTYTPYGTTSMTAALDEVQKHLNDRVNREKAIQLVILMTDGVPNSKYRALEVANKLKQRNVRLAVIGIGQGINHQFNRLIAGCRPREPNCKFYSYADWNEAVALIKPFIAKVCTEVERVANCGPWDPWTACSVTCGRGTHSRSRPSLHEKCTTHMVSECEEGECP 283
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279

Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh........eeeeeeee...eeeee...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......eeeeeeee.....hhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhh..........ee..hhhhhhhhhhhhhh.eeeeeeeeee...............eeeeeee..........eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hqn B  28 VVDEVKYSEEVCNEQVDLYLLVDGSGSIGYPNWITKVIPMLNGLINSLSLSRDTINLYMNLFGSYTTELIRLGSGQSIDKRQALSKVTELRKTYTPYGTTSMTAALDEVQKHLNDRVNREKAIQLVILMTDGVPNSKYRALEVANKLKQRNVRLAVIGIGQGINHQFNRLIAGCRPREPNCKFYSYADWNEAVALIKPFIAKVCTEVERVANCGPWDPWTACSVTCGRGTHSRSRPSLHEKCTTHMVSECEEGECP 283
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277

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 4HQN)

(no "CATH Domain" information available for 4HQN)

(no "Pfam Domain" information available for 4HQN)

Asymmetric Unit(hide GO term definitions)

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
		BGC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FUC	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4hqn)

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
	4hqn
		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
	Q9TVF0_PLAVI \| Q9TVF0
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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
	Q9TVF0_PLAVI \| Q9TVF0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q9TVF0_PLAVI \| Q9TVF0	:	4hql 4hqo

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (6, 6)

SS Bonds (10, 10)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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