Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF SYNAPTOTAGMIN
 
Authors :  P. Strop, M. Vrljic, J. Ernst, A. T. Brunger
Date :  30 May 09  (Deposition) - 23 Feb 10  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Synaptotagmin, Cell Junction, Cytoplasmic Vesicle, Membrane, Metal- Binding, Synapse, Transmembrane, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Vrljic, P. Strop, J. A. Ernst, R. B. Sutton, S. Chu, A. T. Brunger
Molecular Mechanism Of The Synaptotagmin-Snare Interaction In Ca2+-Triggered Vesicle Fusion.
Nat. Struct. Mol. Biol. V. 17 325 2010
PubMed-ID: 20173762  |  Reference-DOI: 10.1038/NSMB.1764

(-) Compounds

Molecule 1 - SYNAPTOTAGMIN-3
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 292-587
    Gene: SYT3
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: SYNAPTOTAGMIN III, SYTIII

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric Unit (2, 21)
No.NameCountTypeFull Name
1CA18Ligand/IonCALCIUM ION
2ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:328 , ASP A:334 , ASP A:386 , PHE A:387 , ASP A:388BINDING SITE FOR RESIDUE CA A 600
02AC2SOFTWAREASP A:388 , SER A:391 , ARG A:392 , ASP A:394 , GLU B:476BINDING SITE FOR RESIDUE CA A 601
03AC3SOFTWAREMET A:459 , ASP A:460 , ASP A:520 , ASP A:522 , GLU A:528BINDING SITE FOR RESIDUE CA A 602
04AC4SOFTWAREASP A:466 , ASN A:490BINDING SITE FOR RESIDUE CA A 603
05AC5SOFTWAREASP A:460 , ASP A:466 , ASP A:520 , TYR A:521 , ASP A:522BINDING SITE FOR RESIDUE CA A 605
06AC6SOFTWARELYS A:327 , ASP A:328 , ASP A:386 , ASP A:388 , ASP A:394 , GLU B:476 , ASN B:511BINDING SITE FOR RESIDUE CA A 606
07AC7SOFTWARECYS A:298 , ASP A:419 , HIS A:543 , GLU A:546BINDING SITE FOR RESIDUE ZN A 700
08AC8SOFTWAREASP B:328 , ASP B:334 , ASP B:386 , PHE B:387 , ASP B:388BINDING SITE FOR RESIDUE CA B 600
09AC9SOFTWAREASP B:388 , SER B:391 , ARG B:392 , ASP B:394 , GLU C:476BINDING SITE FOR RESIDUE CA B 601
10BC1SOFTWAREMET B:459 , ASP B:460 , ASP B:520 , ASP B:522 , GLU B:528BINDING SITE FOR RESIDUE CA B 602
11BC2SOFTWAREASP B:466 , ASN B:490BINDING SITE FOR RESIDUE CA B 603
12BC3SOFTWAREASP B:460 , ASP B:466 , ASP B:520 , TYR B:521 , ASP B:522BINDING SITE FOR RESIDUE CA B 605
13BC4SOFTWARELYS B:327 , ASP B:328 , ASP B:386 , ASP B:388 , ASP B:394 , GLU C:476 , ASN C:511BINDING SITE FOR RESIDUE CA B 606
14BC5SOFTWARECYS B:298 , ASP B:419 , HIS B:543 , GLU B:546BINDING SITE FOR RESIDUE ZN B 700
15BC6SOFTWAREASP C:328 , ASP C:334 , ASP C:386 , PHE C:387 , ASP C:388BINDING SITE FOR RESIDUE CA C 600
16BC7SOFTWAREGLU A:476 , ASP C:388 , SER C:391 , ARG C:392 , ASP C:394BINDING SITE FOR RESIDUE CA C 601
17BC8SOFTWAREMET C:459 , ASP C:460 , ASP C:520 , ASP C:522 , GLU C:528BINDING SITE FOR RESIDUE CA C 602
18BC9SOFTWAREASP C:466 , ASN C:490BINDING SITE FOR RESIDUE CA C 603
19CC1SOFTWAREASP C:460 , ASP C:466 , ASP C:520 , TYR C:521 , ASP C:522BINDING SITE FOR RESIDUE CA C 605
20CC2SOFTWAREGLU A:476 , ASN A:511 , LYS C:327 , ASP C:328 , ASP C:386 , ASP C:388 , ASP C:394BINDING SITE FOR RESIDUE CA C 606
21CC3SOFTWARECYS C:298 , ASP C:419 , HIS C:543 , GLU C:546BINDING SITE FOR RESIDUE ZN C 700

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:523 -A:523
2B:523 -C:523

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Leu A:342 -Pro A:343
2Gln A:410 -Pro A:411
3Leu B:342 -Pro B:343
4Gln B:410 -Pro B:411
5Leu C:342 -Pro C:343
6Gln C:410 -Pro C:411

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HN8)

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C2PS50004 C2 domain profile.SYT3_RAT311-400
 
 
446-534
 
 		  6A:311-400
B:311-400
C:311-400
A:446-534
B:446-534
C:446-534
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C2PS50004 C2 domain profile.SYT3_RAT311-400
 
 
446-534
 
 		  2A:311-400
-
-
A:446-534
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C2PS50004 C2 domain profile.SYT3_RAT311-400
 
 
446-534
 
 		  2-
B:311-400
-
-
B:446-534
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C2PS50004 C2 domain profile.SYT3_RAT311-400
 
 
446-534
 
 		  2-
-
C:311-400
-
-
C:446-534

(-) Exons   (0, 0)

(no "Exon" information available for 3HN8)

(-) 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:279
 aligned with SYT3_RAT | P40748 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:279
                                   304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564         
             SYT3_RAT   295 GAPCGRISFALRYLYGSDQLVVRILQALDLPAKDSNGFSDPYVKIYLLPDRKKKFQTKVHRKTLNPIFNETFQFSVPLAELAQRKLHFSVYDFDRFSRHDLIGQVVLDNLLELAEQPPDRPLWRDILEGGSEKADLGELNFSLCYLPTAGLLTVTIIKASNLKAMDLTGFSDPYVKASLISEGRRLKKRKTSIKKNTLNPTYNEALVFDVAPESVENVGLSIAVVDYDCIGHNEVIGVCRVGPEAADPHGREHWAEMLANPRKPVEHWHQLVEEKTLSS 573
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee....eeeeeeeeee............eeeeeeee.eeeeeee..........eeeeeeee..hhhhh...eeeeeeee.......eeeeeeee.hhhhhhhh.....eeee............eeee..eee....eee..eeeee............eeeeeeeee..eeeeeee..........eeee..eee....hhhhheeeeeeee.......eeeeeeee.....hhhhhhhhhh..........eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------C2  PDB: A:311-400 UniProt: 311-400                                                       ---------------------------------------------C2  PDB: A:446-534 UniProt: 446-534                                                      --------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hn8 A 295 GAPCGRISFALRYLYGSDQLVVRILQALDLPAKDSNGFSDPYVKIYLLPDRKKKFQTKVHRKTLNPIFNETFQFSVPLAELAQRKLHFSVYDFDRFSRHDLIGQVVLDNLLELAEQPPDRPLWRDILEGGSEKADLGELNFSLCYLPTAGLLTVTIIKASNLKAMDLTGFSDPYVKASLISEGRRLKKRKTSIKKNTLNPTYNEALVFDVAPESVENVGLSIAVVDYDCIGHNEVIGVCRVGPEAADPHGREHWAEMLANPRKPVEHWHQLVEEKTLSS 573
                                   304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564         


Chain B from PDB  Type:PROTEIN  Length:279
 aligned with SYT3_RAT | P40748 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:279
                                   304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564         
             SYT3_RAT   295 GAPCGRISFALRYLYGSDQLVVRILQALDLPAKDSNGFSDPYVKIYLLPDRKKKFQTKVHRKTLNPIFNETFQFSVPLAELAQRKLHFSVYDFDRFSRHDLIGQVVLDNLLELAEQPPDRPLWRDILEGGSEKADLGELNFSLCYLPTAGLLTVTIIKASNLKAMDLTGFSDPYVKASLISEGRRLKKRKTSIKKNTLNPTYNEALVFDVAPESVENVGLSIAVVDYDCIGHNEVIGVCRVGPEAADPHGREHWAEMLANPRKPVEHWHQLVEEKTLSS 573
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee....eeeeeeeeee............eeeeeeee.eeeeeee..........eeeeeeee..hhhhh...eeeeeeee.......eeeeeeee.hhhhhhhh.....eeee............eeee..eee....eee..eeeee............eeeeeeeee..eeeeeee..........eeee..eee....hhhhheeeeeeee.......eeeeeeee.....hhhhhhhhhh..........eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------C2  PDB: B:311-400 UniProt: 311-400                                                       ---------------------------------------------C2  PDB: B:446-534 UniProt: 446-534                                                      --------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hn8 B 295 GAPCGRISFALRYLYGSDQLVVRILQALDLPAKDSNGFSDPYVKIYLLPDRKKKFQTKVHRKTLNPIFNETFQFSVPLAELAQRKLHFSVYDFDRFSRHDLIGQVVLDNLLELAEQPPDRPLWRDILEGGSEKADLGELNFSLCYLPTAGLLTVTIIKASNLKAMDLTGFSDPYVKASLISEGRRLKKRKTSIKKNTLNPTYNEALVFDVAPESVENVGLSIAVVDYDCIGHNEVIGVCRVGPEAADPHGREHWAEMLANPRKPVEHWHQLVEEKTLSS 573
                                   304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564         


Chain C from PDB  Type:PROTEIN  Length:279
 aligned with SYT3_RAT | P40748 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:279
                                   304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564         
             SYT3_RAT   295 GAPCGRISFALRYLYGSDQLVVRILQALDLPAKDSNGFSDPYVKIYLLPDRKKKFQTKVHRKTLNPIFNETFQFSVPLAELAQRKLHFSVYDFDRFSRHDLIGQVVLDNLLELAEQPPDRPLWRDILEGGSEKADLGELNFSLCYLPTAGLLTVTIIKASNLKAMDLTGFSDPYVKASLISEGRRLKKRKTSIKKNTLNPTYNEALVFDVAPESVENVGLSIAVVDYDCIGHNEVIGVCRVGPEAADPHGREHWAEMLANPRKPVEHWHQLVEEKTLSS 573
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee....eeeeeeeeee............eeeeeeee.eeeeeee..........eeeeeeee..hhhhh...eeeeeeee.......eeeeeeee.hhhhhhhh.....eeee............eeee..eee....eee..eeeee............eeeeeeeee..eeeeeee..........eeee..eee....hhhhheeeeeeee.......eeeeeeee.....hhhhhhhhhh..........eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------C2  PDB: C:311-400 UniProt: 311-400                                                       ---------------------------------------------C2  PDB: C:446-534 UniProt: 446-534                                                      --------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hn8 C 295 GAPCGRISFALRYLYGSDQLVVRILQALDLPAKDSNGFSDPYVKIYLLPDRKKKFQTKVHRKTLNPIFNETFQFSVPLAELAQRKLHFSVYDFDRFSRHDLIGQVVLDNLLELAEQPPDRPLWRDILEGGSEKADLGELNFSLCYLPTAGLLTVTIIKASNLKAMDLTGFSDPYVKASLISEGRRLKKRKTSIKKNTLNPTYNEALVFDVAPESVENVGLSIAVVDYDCIGHNEVIGVCRVGPEAADPHGREHWAEMLANPRKPVEHWHQLVEEKTLSS 573
                                   304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564
   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)

(no "SCOP Domain" information available for 3HN8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HN8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HN8)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SYT3_RAT | P40748)
molecular function
    GO:0000149    SNARE binding    Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005544    calcium-dependent phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium.
    GO:0030276    clathrin binding    Interacting selectively and non-covalently with a clathrin heavy or light chain, the main components of the coat of coated vesicles and coated pits, and which also occurs in synaptic vesicles.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    GO:0001786    phosphatidylserine binding    Interacting selectively and non-covalently with phosphatidylserine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of L-serine.
    GO:0019905    syntaxin binding    Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse.
biological process
    GO:0017156    calcium ion regulated exocytosis    The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell, induced by a rise in cytosolic calcium-ion levels.
    GO:0048791    calcium ion-regulated exocytosis of neurotransmitter    The release of a neurotransmitter into the synaptic cleft by exocytosis of synaptic vesicles, where the release step is dependent on a rise in cytosolic calcium ion levels.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0031340    positive regulation of vesicle fusion    Any process that activates or increases the frequency, rate or extent of vesicle fusion.
    GO:0017158    regulation of calcium ion-dependent exocytosis    Any process that modulates the frequency, rate or extent of calcium ion-dependent exocytosis.
    GO:0051592    response to calcium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus.
    GO:0016079    synaptic vesicle exocytosis    Fusion of intracellular membrane-bounded vesicles with the pre-synaptic membrane of the neuronal cell resulting in release of neurotransmitter into the synaptic cleft.
cellular component
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070382    exocytic vesicle    A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0098793    presynapse    The part of a synapse that is part of the presynaptic cell.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0030658    transport vesicle membrane    The lipid bilayer surrounding a transport vesicle.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:410 - Pro A:411   [ RasMol ]  
    Gln B:410 - Pro B:411   [ RasMol ]  
    Gln C:410 - Pro C:411   [ RasMol ]  
    Leu A:342 - Pro A:343   [ RasMol ]  
    Leu B:342 - Pro B:343   [ RasMol ]  
    Leu C:342 - Pro C:343   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

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 ](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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3hn8
    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
  SYT3_RAT | P40748
    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
  SYT3_RAT | P40748
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SYT3_RAT | P40748: 1dqv

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3HN8)