4NPJ - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   EXTENDED-SYNAPTOTAGMIN 2, C2A- AND C2B-DOMAINS

Authors :   D. R. Tomchick, J. Rizo, J. Xu

Date :   21 Nov 13 (Deposition) - 29 Jan 14 (Release) - 19 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (1x),B (1x)
Biol. Unit 4: A,B  (1x)

Keywords :   Calcium/Phospholipid Binding Protein, C2 Domain, Membrane Traffic, Protein Targeting, Plasma Membrane, Membrane Protein, Er To Plasma Membrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Xu, T. Bacaj, A. Zhou, D. R. Tomchick, T. C. Sudhof, J. Rizo
Structure And Ca(2+)-Binding Properties Of The Tandem C2 Domains Of E-Syt2.
Structure V. 22 269 2014
PubMed-ID: 24373768 | Reference-DOI: 10.1016/J.STR.2013.11.011
(for further references see the PDB file header)

Molecule 1 - EXTENDED SYNAPTOTAGMIN-2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C2 AND C2B DOMAINS (UNP RESIDUES 363-660)
	Gene	:	ESYT2, EXTENDED-SYNAPTOTAGMIN 2, FAM62B, KIAA1228
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	E-SYT2, CHR2SYT

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A (1x)	B (1x)
Biological Unit 4 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CL	3	Ligand/Ion	CHLORIDE ION
3	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:369 , ARG A:419 , GLU B:585	BINDING SITE FOR RESIDUE CL A 801
2	AC2	SOFTWARE	LYS A:569 , PHE A:591 , HOH A:922	BINDING SITE FOR RESIDUE CL A 802
3	AC3	SOFTWARE	ARG A:546 , GLU A:581 , HOH A:968 , ASP B:462 , ASP B:464 , ASP B:466	BINDING SITE FOR RESIDUE NA B 701
4	AC4	SOFTWARE	LYS B:569 , PHE B:591	BINDING SITE FOR RESIDUE CL B 702
5	AC5	SOFTWARE	TYR B:415 , PHE B:459	BINDING SITE FOR RESIDUE ACT B 703
6	AC6	SOFTWARE	GLU B:443 , ASP B:531 , GLY B:532 , PHE B:591 , HOH B:842	BINDING SITE FOR RESIDUE ACT B 704

(no "SS Bond" information available for 4NPJ)

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

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

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

(no "Exon" information available for 4NPJ)

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:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................eeeeeeeeeee..................eeeeeee..eeee..........eeeeeeeeee......eeeeeeee......eeeeeeeeehhhhhhhheeeeeee.......eeeeeeeeeeee....hhhhhhhhhhhh..........eeeeeeeeeee........eeeeeee..eeee..........eeeeeeeeee......eeeeeeee.....eeeeeeeehhhhhhhhh.eeeeeee........eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4npj A 363 NRITVPLVSEVQIAQLRFPVPKGVLRIHFIEAQDLQGKDTYLKGLVKGKSDPYGIIRVGNQIFQSRVIKENLSPKWNEVYEALVYEHPGQELEIELFDEDPDKDDFLGSLMIDLIEVEKERLLDEWFTLDEVPKGKLHLRLEWLTLMPNASNLDKVLTDIKADKDQANDGLSSALLILYLDSARNLPSGNPNPVVQMSVGHKAQESKIRYKTNEPVWEENFTFFIHNPKRQDLEVEVRDEQHQCSLGNLKVPLSQLLTSEDMTVSQRFQLSNSGPNSTIKMKIALRVLHLEK 659
                                   372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       557       567       577       587       597       607       617       627       637       647       657  
                                                                                                                                                                                                                      551|                                                                                                      
                                                                                                                                                                                                                       557

Chain B from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................eeeeeeeeeee...........eeeeeee..eeee..........eeeeeeeeee......eeeeeeee......eeeeeeeeehhhhhhhheeeeeee.......eeeeeeeeeeee....hhhhhhhhhhh...........eeeeeeeeeee......eeeeee....eee..........eeeeeeeeee......eeeeeeee....eeeeeeeee.hhhhhhhh.eeeeeee........eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4npj B 364 RITVPLVSEVQIAQLRFPVPKGVLRIHFIEAQDLQGKDTGKSDPYGIIRVGNQIFQSRVIKENLSPKWNEVYEALVYEHPGQELEIELFDEDPDKDDFLGSLMIDLIEVEKERLLDEWFTLDEVPKGKLHLRLEWLTLMPNASNLDKVLTDIKADKDQANDGLSSALLILYLDSARNLPNPNPVVQMSVGHKAQESKIRYKTNEPVWEENFTFFIHNPKRQDLEVEVRDEQHQCSLGNLKVPLSQLLTSEDMTVSQRFQLSNSGPNSTIKMKIALRVLHLEK 659
                                   373       383       393       410       420       430       440       450       460       470       480       490       500       510       520       530       540       557       567       577       587       597       607       617       627       637       647       657  
                                                                402|                                                                                                                                        549|                                                                                                      
                                                                 410                                                                                                                                         557

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 4NPJ)

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

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

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
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		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 4npj)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ 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 \| Biol. Unit 3 PNG format \| Biol. Unit 4 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
	4npj
		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
	ESYT2_HUMAN \| A0FGR8
		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
	ESYT2_HUMAN \| A0FGR8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ESYT2_HUMAN \| A0FGR8	:	2dmg 4npk 4p42

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

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 (21, 21)

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