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(-) Description

Title :  CRYSTAL STRUCTURE OF INFLUENZA B VIRUS HEMAGGLUTININ IN COMPLEX WITH LSTC RECEPTOR ANALOG
 
Authors :  Q. Wang, X. Tian, X. Chen, J. Ma
Date :  01 Oct 07  (Deposition) - 05 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Influenza, Receptor Specificity, Human Receptor Analog, Envelope Protein, Fusion Protein, Hemagglutinin, Membrane, Transmembrane, Virion, Glycoprotein, Lipoprotein, Palmitate, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Wang, X. Tian, X. Chen, J. Ma
Structural Basis For Receptor Specificity Of Influenza B Virus Hemagglutinin.
Proc. Natl. Acad. Sci. Usa V. 104 16874 2007
PubMed-ID: 17942670  |  Reference-DOI: 10.1073/PNAS.0708363104

(-) Compounds

Molecule 1 - INFLUENZA B HEMAGGLUTININ (HA)
    ChainsA
    EngineeredYES
    Expression SystemINFLUENZA B VIRUS
    Expression System Taxid11520
    GeneHEMAGGLUTININ
    Organism ScientificINFLUENZA B VIRUS (STRAIN B/HONG KONG/8/73)
    Organism Taxid11531
    StrainB/HONGKONG/8/73
 
Molecule 2 - INFLUENZA B HEMAGGLUTININ (HA)
    ChainsB
    EngineeredYES
    Expression SystemINFLUENZA B VIRUS
    Expression System Taxid11520
    GeneHEMAGGLUTININ
    Organism ScientificINFLUENZA B VIRUS (STRAIN B/HONG KONG/8/73)
    Organism Taxid11531
    StrainB/HONGKONG/8/73

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SIA1Ligand/IonO-SIALIC ACID
Biological Unit 1 (3, 42)
No.NameCountTypeFull Name
1GAL3Ligand/IonBETA-D-GALACTOSE
2NAG36Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:12 , PRO A:13 , ASN A:25 , TYR A:334 , NAG A:344BINDING SITE FOR RESIDUE NAG A 343
02AC2SOFTWARENAG A:343BINDING SITE FOR RESIDUE NAG A 344
03AC3SOFTWAREASN A:123 , ALA A:127 , VAL A:137 , GLN A:268 , NAG A:346BINDING SITE FOR RESIDUE NAG A 345
04AC4SOFTWARENAG A:345BINDING SITE FOR RESIDUE NAG A 346
05AC5SOFTWAREASN A:145 , GLY A:149 , ASN A:150BINDING SITE FOR RESIDUE NAG A 347
06AC6SOFTWAREGLU A:289 , ASN A:301 , NAG A:350BINDING SITE FOR RESIDUE NAG A 349
07AC7SOFTWARENAG A:349BINDING SITE FOR RESIDUE NAG A 350
08AC9SOFTWAREASN A:163BINDING SITE FOR RESIDUE NAG A 348
09AD1SOFTWAREASN A:330 , NAG A:352 , TRP B:21 , ILE B:45 , THR B:49BINDING SITE FOR RESIDUE NAG A 351
10BC1SOFTWARENAG A:351BINDING SITE FOR RESIDUE NAG A 352
11BC2SOFTWAREASN B:145 , THR B:147BINDING SITE FOR RESIDUE NAG B 170
12BC3SOFTWARETHR A:139 , SER A:140 , GLY A:141 , VAL A:160 , ASP A:193 , GLN A:197 , LEU A:201 , PRO A:238 , SER A:240 , GAL A:802 , NAG A:803BINDING SITE FOR RESIDUE SIA A 801
13BC4SOFTWARESIA A:801 , GAL A:802BINDING SITE FOR RESIDUE NAG A 803
14BC5SOFTWAREPRO A:238 , SIA A:801 , NAG A:803BINDING SITE FOR RESIDUE GAL A 802

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:4 -B:137
2A:54 -A:57
3A:60 -A:72
4A:94 -A:143
5A:178 -A:272
6A:292 -A:318
7B:144 -B:148

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RFU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RFU)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RFU)

(-) 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:342
 aligned with HEMA_INBHK | P03462 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:342
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348  
           HEMA_INBHK     9 DRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTQTRGKLCPNCLNCTDLDVALGRPKCMGNIPSAKASILHEVKPGTSGCFPIMHDRTKIRQLPNLLRGYENIRLSARNVTNAETAPGGPYIVGTSGSCPNVTNGNGFFATMAWAVPKNKTATNPLTVEVPYICTKGEDQITVWGFHSDDETQMVKLYGDSKPQKFTSSANGVTTHYVSQIGGFPNQAEDEGLPQSGRIVVDYMVQKPGKTGTIAYQRGVLLPQKVWCASGRRKVIEGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPAKLLK 350
               SCOP domains d2rfua_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee......eeee.....eeee..eee...........ee....ee..........hhhhhhhh............eee..............hhhhhhhhhhhhhhhheeeee................eeee.................eeeeee........eee..........eeeeeeeeee.hhhhhhhhh......eeeeee..eeeeee...................eeeeeeeee.....eeeee...eeee...eeeeee.eee........ee.eee...eee.....ee......eee...ee.....eee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2rfu A   1 DRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTQTRGKLCPNCLNCTDLDVALGRPKCMGTIPSAKASILHEVKPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSARNVTNAETAPGGPYIVGTSGSCPNVTNGNGFFATMAWAVPKNKTATNPLTVEVPYICTKGEDQITVWGFHSDDETQMVKLYGDSKPQKFTSSANGVTTHYVSQIGGFPNQAEDEGLPQSGRIVVDYMVQKPGKTGTIAYQRGVLLPQKVWCASGRSKVIKGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPAKLLK 342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  

Chain A from PDB  Type:PROTEIN  Length:342
 aligned with Q84097_9INFB | Q84097 from UniProtKB/TrEMBL  Length:582

    Alignment length:342
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355  
         Q84097_9INFB    16 DRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTQTRGKLCPNCLNCTDLDVALGRPKCMGTIPSAKASILHEVKPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSARNVTNAETAPGGPYIVGTSGSCPNVTNGNGFFATMAWAVPKNKTATNPLTVEVPYICTKGEDQITVWGFHSDDETQMVKLYGDSKPQKFTSSANGVTTHYVSQIGGFPNQAEDEGLPQSGRIVVDYMVQKPGKTGTIAYQRGVLLPQKVWCASGRSKVIKGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPAKLLK 357
               SCOP domains d2rfua_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee......eeee.....eeee..eee...........ee....ee..........hhhhhhhh............eee..............hhhhhhhhhhhhhhhheeeee................eeee.................eeeeee........eee..........eeeeeeeeee.hhhhhhhhh......eeeeee..eeeeee...................eeeeeeeee.....eeeee...eeee...eeeeee.eee........ee.eee...eee.....ee......eee...ee.....eee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2rfu A   1 DRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTQTRGKLCPNCLNCTDLDVALGRPKCMGTIPSAKASILHEVKPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSARNVTNAETAPGGPYIVGTSGSCPNVTNGNGFFATMAWAVPKNKTATNPLTVEVPYICTKGEDQITVWGFHSDDETQMVKLYGDSKPQKFTSSANGVTTHYVSQIGGFPNQAEDEGLPQSGRIVVDYMVQKPGKTGTIAYQRGVLLPQKVWCASGRSKVIKGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPAKLLK 342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with HEMA_INBHK | P03462 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:169
                                   362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512         
           HEMA_INBHK   353 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLFSLSELEVKNLHRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFNAGEFSLPTFDS 521
               SCOP domains d2rfub_ B: Influenza hemagglutinin (stalk)                                                                                                                                SCOP domains
               CATH domains 2rfuB00 B:1-169  [code=3.90.20.10, no name defined]                                                                                                                       CATH domains
           Pfam domains (1) Hemagglutinin-2rfuB01 B:1-169                                                                                                                                             Pfam domains (1)
           Pfam domains (2) Hemagglutinin-2rfuB02 B:1-169                                                                                                                                             Pfam domains (2)
         Sec.struct. author hhhhhhh..............eeeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee.....hhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rfu B   1 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVDIGNGCFETKHKCNQTCLDRIAAGTFNAGEFSLPTFDS 169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with Q84097_9INFB | Q84097 from UniProtKB/TrEMBL  Length:582

    Alignment length:169
                                   369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519         
         Q84097_9INFB   360 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVDIGNGCFETKHKCNQTCLDRIAAGTFNAGEFSLPTFDS 528
               SCOP domains d2rfub_ B: Influenza hemagglutinin (stalk)                                                                                                                                SCOP domains
               CATH domains 2rfuB00 B:1-169  [code=3.90.20.10, no name defined]                                                                                                                       CATH domains
           Pfam domains (1) Hemagglutinin-2rfuB01 B:1-169                                                                                                                                             Pfam domains (1)
           Pfam domains (2) Hemagglutinin-2rfuB02 B:1-169                                                                                                                                             Pfam domains (2)
         Sec.struct. author hhhhhhh..............eeeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee.....hhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rfu B   1 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVDIGNGCFETKHKCNQTCLDRIAAGTFNAGEFSLPTFDS 169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (14, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HEMA_INBHK | P03462)
molecular function
    GO:0046789    host cell surface receptor binding    Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
    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:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    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: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: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.

Chain A,B   (Q84097_9INFB | Q84097)
molecular function
    GO:0046789    host cell surface receptor binding    Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
    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:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    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: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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        HEMA_INBHK | P034622rft 3bt6
        Q84097_9INFB | Q840972rft 3bt6

(-) Related Entries Specified in the PDB File

2rft 2RFT IS THE SAME PROTEIN IN COMPLEX WITH LSTA RECEPTOR ANALOG