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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EBOLA VIRUS MEMBRANE-FUSION SUBUNIT, GP2, FROM THE ENVELOPE GLYCOPROTEIN ECTODOMAIN
 
Authors :  W. Weissenhorn, A. Carfi, K. H. Lee, J. J. Skehel, D. C. Wiley
Date :  03 Nov 98  (Deposition) - 02 Jul 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Keywords :  Membrane Fusion Subunit, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Weissenhorn, A. Carfi, K. H. Lee, J. J. Skehel, D. C. Wiley
Crystal Structure Of The Ebola Virus Membrane Fusion Subunit, Gp2, From The Envelope Glycoprotein Ectodomain.
Mol. Cell V. 2 605 1998
PubMed-ID: 9844633  |  Reference-DOI: 10.1016/S1097-2765(00)80159-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentGCN4 IS RESIDUE 3 - 32, GP2 IS RESIDUE 51 - 133
    MutationYES
    Organism ScientificEBOLA VIRUS SP.
    Organism Taxid205488

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)ABC   
Biological Unit 2 (1x)   DEF
Biological Unit 3 (1x)A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:112 , HIS D:127BINDING SITE FOR RESIDUE ZN D 150
2AC2SOFTWAREHIS C:112 , GLN F:3BINDING SITE FOR RESIDUE ZN F 150
3AC3SOFTWAREGLN A:3 , HIS E:112BINDING SITE FOR RESIDUE ZN A 150
4AC4SOFTWARESER D:82 , ASN D:85 , SER F:82BINDING SITE FOR RESIDUE CL D 151
5AC5SOFTWAREASN A:85 , SER B:82 , ASN B:85 , SER C:82BINDING SITE FOR RESIDUE CL B 150

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:100 -A:107
2B:100 -B:107
3C:100 -C:107
4D:100 -D:107
5E:100 -E:107
6F:100 -F:107

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EBO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 6)

Asymmetric Unit (1, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_VGP_EBOG4_006 *A474TVGP_EBOG4  ---  ---A/B/C/D/E/FL12T
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_VGP_EBOG4_006 *A474TVGP_EBOG4  ---  ---A/B/CL12T
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_VGP_EBOG4_006 *A474TVGP_EBOG4  ---  ---D/E/FL12T
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_VGP_EBOG4_006 *A474TVGP_EBOG4  ---  ---A/B/C/D/E/FL12T
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EBO)

(-) Exons   (0, 0)

(no "Exon" information available for 1EBO)

(-) 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:112
 aligned with VGP_EBOG4 | O11457 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:169
                                   474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624         
            VGP_EBOG4   465 HHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRREAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYIEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVDK 633
               SCOP domains d1eboa_ A:   Core structure o                              f E                         bo gp2                                                                             SCOP domains
               CATH domains 1eboA00 A:3  -132  [code=1.10                              .28                         7.210, no name defined]                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh--hhhhhhhhhhhhhhhh------------------------------hhh-------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh..hhhhhhhhhh......hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------T--------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ebo A   3 QIEDKIEEILS--KIYHIENEIARIKKLI------------------------------GEA-------------------------DGLIEGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCRIEPHDWTKNITDKIDQIIHDFVDK 132
                                    12|  |    20        |-         -         -        30 |       -         -       |53        63        73        83        93       103       113       123         
                                     13 14             29                             30 |                        51                                                                                 
                                                                                        32                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:112
 aligned with VGP_EBOG4 | O11457 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:169
                                   474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624         
            VGP_EBOG4   465 HHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRREAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYIEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVDK 633
               SCOP domains d1ebob_ B:   Core structure o                              f E                         bo gp2                                                                             SCOP domains
               CATH domains 1eboB00 B:3  -132  [code=1.10                              .28                         7.210, no name defined]                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh--hhhhhhhhhhhhhhhh------------------------------h..-------------------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh..hhhhh.hhhh......hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------T--------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ebo B   3 QIEDKIEEILS--KIYHIENEIARIKKLI------------------------------GEA-------------------------DGLIEGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCRIEPHDWTKNITDKIDQIIHDFVDK 132
                                    12|  |    20        |-         -         -        30 |       -         -       |53        63        73        83        93       103       113       123         
                                     13 14             29                             30 |                        51                                                                                 
                                                                                        32                                                                                                           

Chain C from PDB  Type:PROTEIN  Length:111
 aligned with VGP_EBOG4 | O11457 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:168
                                   474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624        
            VGP_EBOG4   465 HHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRREAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYIEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVD 632
               SCOP domains d1eboc_ C:   Core structure o                              f E                         bo gp2                                                                            SCOP domains
               CATH domains 1eboC00 C:3  -131  [code=1.10                              .28                         7.210, no name defined]                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh--hhhhhhhhhhhhhhhh------------------------------hhh-------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhh..hhhh......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------T-------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ebo C   3 QIEDKIEEILS--KIYHIENEIARIKKLI------------------------------GEA-------------------------DGLIEGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCRIEPHDWTKNITDKIDQIIHDFVD 131
                                    12|  |    20        |-         -         -        30 |       -         -       |53        63        73        83        93       103       113       123        
                                     13 14             29                             30 |                        51                                                                                
                                                                                        32                                                                                                          

Chain D from PDB  Type:PROTEIN  Length:112
 aligned with VGP_EBOG4 | O11457 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:169
                                   474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624         
            VGP_EBOG4   465 HHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRREAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYIEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVDK 633
               SCOP domains d1ebod_ D:   Core structure o                              f E                         bo gp2                                                                             SCOP domains
               CATH domains 1eboD00 D:3  -132  [code=1.10                              .28                         7.210, no name defined]                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh--hhhhhhhhhhhhhhhh------------------------------hhh-------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhh......hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------T--------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ebo D   3 QIEDKIEEILS--KIYHIENEIARIKKLI------------------------------GEA-------------------------DGLIEGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCRIEPHDWTKNITDKIDQIIHDFVDK 132
                                    12|  |    20        |-         -         -        30 |       -         -       |53        63        73        83        93       103       113       123         
                                     13 14             29                             30 |                        51                                                                                 
                                                                                        32                                                                                                           

Chain E from PDB  Type:PROTEIN  Length:111
 aligned with VGP_EBOG4 | O11457 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:168
                                   474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624        
            VGP_EBOG4   465 HHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRREAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYIEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVD 632
               SCOP domains d1eboe_ E:   Core structure o                              f E                         bo gp2                                                                            SCOP domains
               CATH domains 1eboE00 E:3  -131  [code=1.10                              .28                         7.210, no name defined]                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh--hhhhhhhhhhhhhhhh------------------------------hhh-------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhh......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------T-------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ebo E   3 QIEDKIEEILS--KIYHIENEIARIKKLI------------------------------GEA-------------------------DGLIEGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCRIEPHDWTKNITDKIDQIIHDFVD 131
                                    12|  |    20        |-         -         -        30 |       -         -       |53        63        73        83        93       103       113       123        
                                     13 14             29                             30 |                        51                                                                                
                                                                                        32                                                                                                          

Chain F from PDB  Type:PROTEIN  Length:113
 aligned with VGP_EBOG4 | O11457 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:170
                                   474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634
            VGP_EBOG4   465 HHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRREAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYIEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVDKT 634
               SCOP domains d1ebof_ F:   Core structure o                              f E                         bo gp2                                                                              SCOP domains
               CATH domains 1eboF00 F:3  -133  [code=1.10                              .28                         7.210, no name defined]                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh--hhhhhhhhhhhhhhhh------------------------------hhh-------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhh......hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------T---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ebo F   3 QIEDKIEEILS--KIYHIENEIARIKKLI------------------------------GEA-------------------------DGLIEGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCRIEPHDWTKNITDKIDQIIHDFVDKT 133
                                    12|  |    20        |-         -         -        30 |       -         -       |53        63        73        83        93       103       113       123       133
                                     13 14             29                             30 |                        51                                                                                  
                                                                                        32                                                                                                            

   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  (1, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (VGP_EBOG4 | O11457)
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0039587    suppression by virus of host tetherin activity    Any process in which a virus stops, prevents, or reduces the activity of host tetherin activity. Tetherin (also known as BST2) is an alpha interferon-inducible cellular factor that impairs the release of many enveloped viruses. By blocking tetherin activity, many viruses circumvent its antiviral effects.
    GO:0039502    suppression by virus of host type I interferon-mediated signaling pathway    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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