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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GAIN AND HORMR DOMAINS OF BRAIN ANGIOGENESIS INHIBITOR 3 (BAI3)
 
Authors :  D. Arac, A. A. Boucard, M. F. Bolliger, J. Nguyen, M. Soltis, T. C. Sudhof A. T. Brunger
Date :  06 Feb 12  (Deposition) - 22 Feb 12  (Release) - 16 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gain Domain, Includes Gps Motif, Autoproteolytic Fold, Extracellular, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Arac, A. A. Boucard, M. F. Bolliger, J. Nguyen, S. M. Soltis, T. C. Sudhof, A. T. Brunger
A Novel Evolutionarily Conserved Domain Of Cell-Adhesion Gpcrs Mediates Autoproteolysis.
Embo J. V. 31 1364 2012
PubMed-ID: 22333914  |  Reference-DOI: 10.1038/EMBOJ.2012.26

(-) Compounds

Molecule 1 - BRAIN-SPECIFIC ANGIOGENESIS INHIBITOR 3
    ChainsA, B
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System PlasmidPACGP67A
    Expression System Taxid7111
    Expression System Vector TypePLASMID
    FragmentGAIN AND HORMR DOMAINS OF BAI3, UNP RESIDUES 498-868
    GeneBAI3, KIAA0550
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1FUL2Ligand/IonBETA-L-FUCOSE
2GOL9Ligand/IonGLYCEROL
3NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1FUL1Ligand/IonBETA-L-FUCOSE
2GOL5Ligand/IonGLYCEROL
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1FUL1Ligand/IonBETA-L-FUCOSE
2GOL4Ligand/IonGLYCEROL
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:540 , NAG A:902 , FUL A:903BINDING SITE FOR RESIDUE NAG A 901
02AC2SOFTWARENAG A:901 , FUL A:903BINDING SITE FOR RESIDUE NAG A 902
03AC3SOFTWARENAG A:901 , NAG A:902BINDING SITE FOR RESIDUE FUL A 903
04AC4SOFTWAREGLN A:576 , ILE A:579 , GLU A:621 , ASN A:625 , NAG A:905 , HOH A:1061BINDING SITE FOR RESIDUE NAG A 904
05AC5SOFTWARENAG A:904BINDING SITE FOR RESIDUE NAG A 905
06AC6SOFTWARELEU A:532 , SER A:546 , SER A:563 , GLN A:666 , HOH A:1056BINDING SITE FOR RESIDUE GOL A 906
07AC7SOFTWAREPRO A:510 , GLU A:512 , SER A:639 , MET A:689 , SER A:695 , HOH A:1018BINDING SITE FOR RESIDUE GOL A 907
08AC8SOFTWAREHOH A:1016 , PRO B:510 , PRO B:515 , GLU B:516 , TYR B:518 , HOH B:1052BINDING SITE FOR RESIDUE GOL A 908
09AC9SOFTWARELEU A:539 , ASN A:540 , ALA A:541 , GLN B:536 , GLY B:543 , THR B:544BINDING SITE FOR RESIDUE GOL A 909
10BC1SOFTWAREGLU A:659 , ASP A:663 , HOH A:1042 , GLU B:504BINDING SITE FOR RESIDUE GOL A 910
11BC2SOFTWAREASN B:540 , TYR B:612 , NAG B:902 , FUL B:903BINDING SITE FOR RESIDUE NAG B 901
12BC3SOFTWARENAG B:901 , FUL B:903 , HOH B:1058BINDING SITE FOR RESIDUE NAG B 902
13BC4SOFTWAREASN B:610 , NAG B:901 , NAG B:902BINDING SITE FOR RESIDUE FUL B 903
14BC5SOFTWAREGLN B:576 , GLU B:621 , ASN B:625 , GLU B:673BINDING SITE FOR RESIDUE NAG B 904
15BC6SOFTWARETYR A:518 , SER A:521 , HOH A:1099 , ALA B:509 , PRO B:510 , GLU B:516BINDING SITE FOR RESIDUE GOL B 905
16BC7SOFTWAREASP B:663 , GOL B:908BINDING SITE FOR RESIDUE GOL B 906
17BC8SOFTWAREGLU A:756 , PRO B:510 , TYR B:511 , ILE B:513 , PRO B:515 , VAL B:556 , ALA B:557BINDING SITE FOR RESIDUE GOL B 907
18BC9SOFTWAREGLU B:560 , GLN B:561 , PRO B:562 , SER B:563 , ASP B:663 , GLN B:666 , GOL B:906 , HOH B:1048BINDING SITE FOR RESIDUE GOL B 908

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:514 -A:549
2A:537 -A:567
3A:819 -A:851
4A:839 -A:853
5B:502 -B:507
6B:514 -B:549
7B:537 -B:567
8B:819 -B:851
9B:839 -B:853

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:720 -Pro A:721
2Arg A:793 -Pro A:794
3Phe B:720 -Pro B:721
4Arg B:793 -Pro B:794

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_046525N503SAGRB3_HUMANPolymorphism1932618BS503S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (0, 0)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_046525N503SAGRB3_HUMANPolymorphism1932618BS503S

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

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_PROTEIN_RECEP_F2_3PS50227 G-protein coupled receptors family 2 profile 1.AGRB3_HUMAN501-571  1B:501-571
2GPSPS50221 GPS domain profile.AGRB3_HUMAN816-868
 
  2A:816-866
B:816-864
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_PROTEIN_RECEP_F2_3PS50227 G-protein coupled receptors family 2 profile 1.AGRB3_HUMAN501-571  0-
2GPSPS50221 GPS domain profile.AGRB3_HUMAN816-868
 
  1A:816-866
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_PROTEIN_RECEP_F2_3PS50227 G-protein coupled receptors family 2 profile 1.AGRB3_HUMAN501-571  1B:501-571
2GPSPS50221 GPS domain profile.AGRB3_HUMAN816-868
 
  1-
B:816-864

(-) Exons   (0, 0)

(no "Exon" information available for 4DLO)

(-) 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:351
 aligned with AGRB3_HUMAN | O60242 from UniProtKB/Swiss-Prot  Length:1522

    Alignment length:359
                                   517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857         
          AGRB3_HUMAN   508 PAPYEICPEDYLMSMVWKRTPAGDLAFNQCPLNATGTTSRRCSLSLHGVAFWEQPSFARCISNEYRHLQHSIKEHLAKGQRMLAGDGMSQVTKTLLDLTQRKNFYAGDLLMSVEILRNVTDTFKRASYIPASDGVQNFFQIVSNLLDEENKEKWEDAQQIYPGSIELMQVIEDFIHIVGMGMMDFQNSYLMTGNVVASIQKLPAASVLTDINFPMKGRKGMVDWARNSEDRVVIPKSIFTPVSSKELDESSVFVLGAVLYKNLDLILPTLRNYTVINSKIIVVTIRPEPKTTDSFLEIELAHLANGTLNPYCVLWDDSKTNESLGTWSTQGCKTVLTDASHTKCLCDRLSTFAILAQQP 866
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee............ee...eeee.....eeeeeeeeeee.....eee...eeeeeeehhhhhhhhhhhhhhh---.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....eeeee...eeeeeeeee.......eee........hhhhhhh..eeeehhhhhh....--.....eeeeeeeee.hhhhh.......eee...eeeeeee.........eeeeee......eeeeeeeee..---....eee...eeeeeee..eeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE G_PROTEIN_RECEP_F2_3  PDB: - UniProt: 501-571                   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GPS  PDB: A:816-866 UniProt: 816-868                PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dlo A 508 PAPYEICPEDYLMSMVWKRTPAGDLAFNQCPLNATGTTSRRCSLSLHGVAFWEQPSFARCISNEYRHLQHSIKEHLA---RMLAGDGMSQVTKTLLDLTQRKNFYAGDLLMSVEILRNVTDTFKRASYIPASDGVQNFFQIVSNLLDEENKEKWEDAQQIYPGSIELMQVIEDFIHIVGMGMMDFQNSYLMTGNVVASIQKLPAASVLTDINFPMKGRKGMVDWARNSEDRVVIPKSIFTPVSS--LDESSVFVLGAVLYKNLDLILPTLRNYTVINSKIIVVTIRPEPKTTDSFLEIELAHLANGTLNPYCVLWDDS---ESLGTWSTQGCKTVLTDASHTKCLCDRLSTFAILAQQP 866
                                   517       527       537       547       557       567       577      |  -|      597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747   |  |757       767       777       787       797       807       817       | - |     837       847       857         
                                                                                                      584 588                                                                                                                                                                751  |                                                                    825 829                                     
                                                                                                                                                                                                                                                                                754                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:337
 aligned with AGRB3_HUMAN | O60242 from UniProtKB/Swiss-Prot  Length:1522

    Alignment length:364
                                   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860    
          AGRB3_HUMAN   501 RCNEQRCPAPYEICPEDYLMSMVWKRTPAGDLAFNQCPLNATGTTSRRCSLSLHGVAFWEQPSFARCISNEYRHLQHSIKEHLAKGQRMLAGDGMSQVTKTLLDLTQRKNFYAGDLLMSVEILRNVTDTFKRASYIPASDGVQNFFQIVSNLLDEENKEKWEDAQQIYPGSIELMQVIEDFIHIVGMGMMDFQNSYLMTGNVVASIQKLPAASVLTDINFPMKGRKGMVDWARNSEDRVVIPKSIFTPVSSKELDESSVFVLGAVLYKNLDLILPTLRNYTVINSKIIVVTIRPEPKTTDSFLEIELAHLANGTLNPYCVLWDDSKTNESLGTWSTQGCKTVLTDASHTKCLCDRLSTFAILAQ 864
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhh.ee...hhhhh....ee...eeeee....eeeeeeeeeee.....eee...eeeeeeehhhhhhhhhhhhh-------.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....eeeee...eeeeeeeee.......eee........hhhhhh..eeeeehhhhh.----------.eeeeeeeee.hhhhh........ee...eeeeeee...----..eeeeee......eeeeeeeee.------..eee...eeee.....eeeeee....eeeeeee Sec.struct. author
                 SAPs(SNPs) --S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE G_PROTEIN_RECEP_F2_3  PDB: B:501-571 UniProt: 501-571                  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GPS  PDB: B:816-864 UniProt: 816-868              PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dlo B 501 RCSEQRCPAPYEICPEDYLMSMVWKRTPAGDLAFNQCPLNATGTTSRRCSLSLHGVAFWEQPSFARCISNEYRHLQHSIKEH-------LAGDGMSQVTKTLLDLTQRKNFYAGDLLMSVEILRNVTDTFKRASYIPASDGVQNFFQIVSNLLDEENKEKWEDAQQIYPGSIELMQVIEDFIHIVGMGMMDFQNSYLMTGNVVASIQKLPAASVLTDINFPMKGRKGMVDWARNSEDRVVIPKSIFT----------SVFVLGAVLYKNLDLILPTLRNYTVINSKIIVVTIRPEP----SFLEIELAHLANGTLNPYCVLWDD------LGTWSTQGCKTVLTDASHTKCLCDRLSTFAILAQ 864
                                   510       520       530       540       550       560       570       580 |     590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740      |  -       760       770       780       790     |   -|      810       820   |     -|      840       850       860    
                                                                                                           582     590                                                                                                                                                          747        758                                   796  801                    824    831                                 

   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 4DLO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (AGRB3_HUMAN | O60242)
molecular function
    GO:0004930    G-protein coupled receptor activity    Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0007520    myoblast fusion    A process in which non-proliferating myoblasts fuse to existing fibers or to myotubes to form new fibers. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
    GO:0016525    negative regulation of angiogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0051965    positive regulation of synapse assembly    Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
    GO:0048814    regulation of dendrite morphogenesis    Any process that modulates the frequency, rate or extent of dendrite morphogenesis.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    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.

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(-) Related Entries Specified in the PDB File

4dlq CRYSTAL STRUCTURE OF THE GAIN AND HORMR DOMAINS OF CIRL 1/ LATROPHILIN 1 (CL1)