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(-) Description

Title :  NIPAH VIRUS ATTACHMENT GLYCOPROTEIN
 
Authors :  T. A. Bowden, M. Crispin, D. J. Harvey, A. R. Aricescu, J. M. Grimes, E. Y. D. I. Stuart
Date :  20 Jun 08  (Deposition) - 07 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Transmembrane, Viral Attachment, Envelope Protein, Paramyxovirus, Signal-Anchor, Hemagglutinin, Niv, Hev, Nipah, Hev-G, Virus, Niv-G, Hendra, Virion, Membrane, Henipavirus, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. A. Bowden, M. Crispin, D. J. Harvey, A. R. Aricescu, J. M. Grimes, E. Y. Jones, D. I. Stuart
Crystal Structure And Carbohydrate Analysis Of Nipah Virus Attachment Glycoprotein: A Template For Antiviral And Vaccine Design.
J. Virol. V. 82 11628 2008
PubMed-ID: 18815311  |  Reference-DOI: 10.1128/JVI.01344-08

(-) Compounds

Molecule 1 - HEMAGGLUTININ-NEURAMINIDASE
    ChainsA, B
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHUMAN EMBRYONIC KIDNEY 293T
    Expression System PlasmidPHLSEC
    Expression System StrainCRL-1573
    Expression System Taxid9606
    FragmentRECEPTOR-BINDING DOMAIN, RESIDUES 183-602
    Organism ScientificNIPAH VIRUS
    Organism Taxid121791
    Other DetailsSYNTHETICALLY OPTIMIZED CDNA (GENEART)
    SynonymNIV-G

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GBL8Ligand/IonGAMMA-BUTYROLACTONE
3NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GBL6Ligand/IonGAMMA-BUTYROLACTONE
3NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GBL2Ligand/IonGAMMA-BUTYROLACTONE
3NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR B:299 , SER B:311BINDING SITE FOR RESIDUE CL B1603
02AC2SOFTWAREARG B:344 , LEU B:370 , LYS B:376 , HOH B:2152BINDING SITE FOR RESIDUE CL B1604
03AC3SOFTWARESER A:447 , LEU A:448 , PHE A:566 , ILE A:572 , HOH A:2276 , HOH A:2288BINDING SITE FOR RESIDUE GBL A1603
04AC4SOFTWAREPRO A:323 , SER A:325BINDING SITE FOR RESIDUE GBL A1604
05AC5SOFTWARETYR A:377 , ASN A:381 , PRO A:383 , ASP A:433 , ARG A:435 , LEU A:436 , HOH A:2107 , HOH A:2171 , HOH A:2174BINDING SITE FOR RESIDUE GBL A1605
06AC6SOFTWAREGLU A:254 , LEU A:256 , HOH A:2289BINDING SITE FOR RESIDUE GBL A1606
07AC7SOFTWAREPHE A:458 , TRP A:504 , GLU A:505 , GLY A:506BINDING SITE FOR RESIDUE GBL A1607
08AC8SOFTWAREPHE B:458 , TRP B:504 , GLU B:505 , GLY B:506 , HOH B:2278BINDING SITE FOR RESIDUE GBL B1605
09AC9SOFTWAREMET A:267 , THR A:268 , ASN A:269 , VAL A:270BINDING SITE FOR RESIDUE GBL A1608
10BC1SOFTWARELEU B:448 , PHE B:512 , LEU B:513 , ILE B:514 , CYS B:565 , LEU B:567 , HOH B:2262BINDING SITE FOR RESIDUE GBL B1606
11BC2SOFTWAREASN B:378 , ASN B:381 , HOH B:2121 , HOH B:2280BINDING SITE FOR RESIDUE NAG B1607
12BC3SOFTWAREASN A:478 , ASN A:481 , HOH A:2206 , HOH A:2211BINDING SITE FOR RESIDUE NAG A1609
13BC4SOFTWARETHR A:361 , LYS A:415 , ASN A:417 , SER A:419 , HOH A:2290BINDING SITE FOR RESIDUE NAG A1610
14BC5SOFTWAREVAL B:300 , ASN B:306 , TYR B:309 , HOH B:2047 , HOH B:2281 , HOH B:2282BINDING SITE FOR RESIDUE NAG B1608
15BC6SOFTWARETHR B:361 , LYS B:415 , ASN B:417 , HOH B:2095BINDING SITE FOR RESIDUE NAG B1609
16BC7SOFTWAREASN B:529 , HOH B:2285BINDING SITE FOR RESIDUE NAG B1610
17BC8SOFTWAREASN A:529 , HOH A:2220BINDING SITE FOR RESIDUE NAG A1611
18BC9SOFTWAREASN B:478 , TRP B:479 , ARG B:480 , ASN B:481 , HOH B:2286BINDING SITE FOR RESIDUE NAG B1611
19CC1SOFTWAREASN A:378 , SER A:380 , ASN A:381BINDING SITE FOR RESIDUE NAG A1612
20CC2SOFTWAREVAL A:300 , GLY A:301 , ASN A:306 , TYR A:309 , ARG B:242BINDING SITE FOR RESIDUE NAG A1613

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:189 -A:601
2A:216 -A:240
3A:282 -A:295
4A:382 -A:395
5A:387 -A:499
6A:493 -A:503
7A:565 -A:574
8B:189 -B:601
9B:216 -B:240
10B:282 -B:295
11B:382 -B:395
12B:387 -B:499
13B:493 -B:503
14B:565 -B:574

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asn A:473 -Pro A:474
2Asn B:473 -Pro B:474
3Gly B:584 -Asp B:585

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 16)

Asymmetric Unit (8, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_GLYCP_NIPAV_004 *R248KGLYCP_NIPAV  ---  ---A/BR248K
2UniProtVAR_GLYCP_NIPAV_005 *T272AGLYCP_NIPAV  ---  ---A/BT272A
3UniProtVAR_GLYCP_NIPAV_006 *G327DGLYCP_NIPAV  ---  ---A/BG327D
4UniProtVAR_GLYCP_NIPAV_007 *I408VGLYCP_NIPAV  ---  ---A/BI408V
5UniProtVAR_GLYCP_NIPAV_008 *V426IGLYCP_NIPAV  ---  ---A/BV426I
6UniProtVAR_GLYCP_NIPAV_009 *L470QGLYCP_NIPAV  ---  ---A/BL470Q
7UniProtVAR_GLYCP_NIPAV_010 *N478SGLYCP_NIPAV  ---  ---A/BN478S
8UniProtVAR_GLYCP_NIPAV_011 *N481DGLYCP_NIPAV  ---  ---A/BN481D
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_GLYCP_NIPAV_004 *R248KGLYCP_NIPAV  ---  ---AR248K
2UniProtVAR_GLYCP_NIPAV_005 *T272AGLYCP_NIPAV  ---  ---AT272A
3UniProtVAR_GLYCP_NIPAV_006 *G327DGLYCP_NIPAV  ---  ---AG327D
4UniProtVAR_GLYCP_NIPAV_007 *I408VGLYCP_NIPAV  ---  ---AI408V
5UniProtVAR_GLYCP_NIPAV_008 *V426IGLYCP_NIPAV  ---  ---AV426I
6UniProtVAR_GLYCP_NIPAV_009 *L470QGLYCP_NIPAV  ---  ---AL470Q
7UniProtVAR_GLYCP_NIPAV_010 *N478SGLYCP_NIPAV  ---  ---AN478S
8UniProtVAR_GLYCP_NIPAV_011 *N481DGLYCP_NIPAV  ---  ---AN481D
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_GLYCP_NIPAV_004 *R248KGLYCP_NIPAV  ---  ---BR248K
2UniProtVAR_GLYCP_NIPAV_005 *T272AGLYCP_NIPAV  ---  ---BT272A
3UniProtVAR_GLYCP_NIPAV_006 *G327DGLYCP_NIPAV  ---  ---BG327D
4UniProtVAR_GLYCP_NIPAV_007 *I408VGLYCP_NIPAV  ---  ---BI408V
5UniProtVAR_GLYCP_NIPAV_008 *V426IGLYCP_NIPAV  ---  ---BV426I
6UniProtVAR_GLYCP_NIPAV_009 *L470QGLYCP_NIPAV  ---  ---BL470Q
7UniProtVAR_GLYCP_NIPAV_010 *N478SGLYCP_NIPAV  ---  ---BN478S
8UniProtVAR_GLYCP_NIPAV_011 *N481DGLYCP_NIPAV  ---  ---BN481D
   * ID not provided by source

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VWD)

(-) Exons   (0, 0)

(no "Exon" information available for 2VWD)

(-) 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:413
 aligned with GLYCP_NIPAV | Q9IH62 from UniProtKB/Swiss-Prot  Length:602

    Alignment length:416
                                   196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596      
          GLYCP_NIPAV   187 NICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSCSRGVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGDPILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTLYFPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGENPKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNNTVISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKDNEILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQCT 602
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee..-.........eeeeeeeeeee..eeeeeeeeee...--..eeeeeeeeeeeee.....eeeeeeeee...hhh.eeeeeeeee..eeeeeeee........hhhhh...eeeeeee......hhhh.eeee....ee.....eeee.....eee..eeeeeeeeeee.hhh..hhhhh..........hhhhhh........eeeeeeeeeee........eeeee...........eeeeee..eeeeee.........eeeeeee....eeee...............................eeeee....eeeeeee........eeeeeee..eeeeeee......eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------K-----------------------A------------------------------------------------------D--------------------------------------------------------------------------------V-----------------I-------------------------------------------Q-------S--D------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vwd A 187 NICLQKTSNQILKPKLIS-TLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSC--GVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGDPILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTLYFPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGENPKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNNTVISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKDNEILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQCT 602
                                   196       206       216       226       236   |  |246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596      
                                           204 |                               240  |                                                                                                                                                                                                                                                                                                                                                                       
                                             206                                  243                                                                                                                                                                                                                                                                                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:410
 aligned with GLYCP_NIPAV | Q9IH62 from UniProtKB/Swiss-Prot  Length:602

    Alignment length:416
                                   196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596      
          GLYCP_NIPAV   187 NICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSCSRGVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGDPILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTLYFPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGENPKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNNTVISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKDNEILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQCT 602
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) HN-2vwdB01 B:187-601                                                                                                                                                                                                                                                                                                                                                                                                           - Pfam domains (1)
           Pfam domains (2) HN-2vwdB02 B:187-601                                                                                                                                                                                                                                                                                                                                                                                                           - Pfam domains (2)
         Sec.struct. author ..............ee.hhhh.------.eeeeeeeeee..eeeeeeeee........eeeeeeeeeeeee.....eeeeeeeee.......eeeeeeeee..eeeeeeee................eeeeeee......hhhh.eeee....ee.....eeee.....eee..eeeeeeeeeee.hhh..hhhhh..........hhhhhh........eeeeeeeeeee........eeeee...........eeeeee..eeeeee.........eeeeeee....eeee...............................eeeee....eeeeeee........eeeeeee..eeeeeee.......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------K-----------------------A------------------------------------------------------D--------------------------------------------------------------------------------V-----------------I-------------------------------------------Q-------S--D------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vwd B 187 NICLQKTSNQILKPKLISYTLP------TCITDPLLAMDEGYFAYSHLERIGSCSRGVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGDPILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTLYFPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGENPKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNNTVISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKDNEILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQCT 602
                                   196       206 |     216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596      
                                               208    215                                                                                                                                                                                                                                                                                                                                                                                                   

   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 2VWD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VWD)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: HN (6)
1aHN-2vwdB01B:187-601
1bHN-2vwdB02B:187-601

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GLYCP_NIPAV | Q9IH62)
molecular function
    GO:0004308    exo-alpha-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
    GO:0046789    host cell surface receptor binding    Interacting selectively and non-covalently with a receptor on the host cell surface.
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: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:0019058    viral life cycle    A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
    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: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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        GLYCP_NIPAV | Q9IH622vsm 3d11 3d12

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2vsm NIPAH VIRUS ATTACHMENT GLYCOPROTEIN IN COMPLEX WITH HUMAN CELL SURFACE RECEPTOR EPHRINB2