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

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GROWTH AND DIFFERENTIATION FACTOR 5 (GDF5)
 
Authors :  H. Schreuder, A. Liesum, J. Pohl, M. Kruse, M. Koyama
Date :  12 Jan 05  (Deposition) - 11 Mar 05  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Growth Factor, Growth Differentiation Factor, Bone Morphogenetic Factor, Hormone-Receptor Interaction, Cystine Knot, Preformed Receptor Dimer, Cytokine, Dwarfism, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Schreuder, A. Liesum, J. Pohl, M. Kruse, M. Koyama
Crystal Structure Of Recombinant Human Growth Differentiation Factor 5. Evidence For Interaction Of The Type I And Type Ii Receptor Binding Sites.
Biochem. Biophys. Res. Commun. V. 329 1076 2005
PubMed-ID: 15752764  |  Reference-DOI: 10.1016/J.BBRC.2005.02.078

(-) Compounds

Molecule 1 - GROWTH DIFFERENTIATION FACTOR 5
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUC18
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsINTERCHAIN DISULFIDE LINK BETWEEN TWO CRYSTALLOGRAPHICALLY RELATED MONOMERS
    SynonymGDF-5, CARTILAGE-DERIVED MORPHOGENETIC PROTEIN 1, CDMP-1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1IPA5Ligand/IonISOPROPYL ALCOHOL
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1IPA10Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:96 , TYR A:108BINDING SITE FOR RESIDUE IPA A 200
2AC2SOFTWAREASN A:63BINDING SITE FOR RESIDUE IPA A 201
3AC3SOFTWAREPRO A:86 , ARG A:119BINDING SITE FOR RESIDUE IPA A 202
4AC4SOFTWAREASP A:29 , SER A:93 , TYR A:105 , IPA A:204BINDING SITE FOR RESIDUE IPA A 203
5AC5SOFTWAREIPA A:203 , HOH A:2072BINDING SITE FOR RESIDUE IPA A 204

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:18 -A:84
2A:47 -A:116
3A:51 -A:118
4A:83 -A:83

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:38 -Pro A:39
2Phe A:53 -Pro A:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (13, 13)

Asymmetric Unit (13, 13)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_064416R399CGDF5_HUMANDisease (BDA1C)  ---AR17C
02UniProtVAR_017407C400YGDF5_HUMANDisease (AMDG)  ---AC18Y
03UniProtVAR_073141W414RGDF5_HUMANDisease (SYNS2)  ---AW32R
04UniProtVAR_054911P436TGDF5_HUMANDisease (DPS)  ---AP54T
05UniProtVAR_026545R438LGDF5_HUMANDisease (SYM1B)  ---AR56L
06UniProtVAR_037980S439TGDF5_HUMANDisease (DPS)  ---AS57T
07UniProtVAR_037981H440LGDF5_HUMANDisease (DPS)  ---AH58L
08UniProtVAR_017408L441PGDF5_HUMANDisease (SYNS2)28936683AL59P
09UniProtVAR_073142N445KGDF5_HUMANDisease (SYNS2)  ---AN63K
10UniProtVAR_073143N445TGDF5_HUMANDisease (SYNS2)  ---AN63T
11UniProtVAR_037982S475NGDF5_HUMANDisease (SYNS2)  ---AS93N
12UniProtVAR_074162V486MGDF5_HUMANDisease (BDC)  ---AV104M
13UniProtVAR_037983E491KGDF5_HUMANDisease (SYM1B)  ---AE109K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (13, 26)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_064416R399CGDF5_HUMANDisease (BDA1C)  ---AR17C
02UniProtVAR_017407C400YGDF5_HUMANDisease (AMDG)  ---AC18Y
03UniProtVAR_073141W414RGDF5_HUMANDisease (SYNS2)  ---AW32R
04UniProtVAR_054911P436TGDF5_HUMANDisease (DPS)  ---AP54T
05UniProtVAR_026545R438LGDF5_HUMANDisease (SYM1B)  ---AR56L
06UniProtVAR_037980S439TGDF5_HUMANDisease (DPS)  ---AS57T
07UniProtVAR_037981H440LGDF5_HUMANDisease (DPS)  ---AH58L
08UniProtVAR_017408L441PGDF5_HUMANDisease (SYNS2)28936683AL59P
09UniProtVAR_073142N445KGDF5_HUMANDisease (SYNS2)  ---AN63K
10UniProtVAR_073143N445TGDF5_HUMANDisease (SYNS2)  ---AN63T
11UniProtVAR_037982S475NGDF5_HUMANDisease (SYNS2)  ---AS93N
12UniProtVAR_074162V486MGDF5_HUMANDisease (BDC)  ---AV104M
13UniProtVAR_037983E491KGDF5_HUMANDisease (SYM1B)  ---AE109K

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TGF_BETA_1PS00250 TGF-beta family signature.GDF5_HUMAN418-433  1A:36-51
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TGF_BETA_1PS00250 TGF-beta family signature.GDF5_HUMAN418-433  2A:36-51

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003743721ENSE00001463325chr20:34042568-34042462107GDF5_HUMAN-00--
1.2ENST000003743722ENSE00001463324chr20:34029194-34029039156GDF5_HUMAN-00--
1.3bENST000003743723bENSE00001463323chr20:34025949-34025078872GDF5_HUMAN1-2112110--
1.4ENST000003743724ENSE00001463322chr20:34022581-340211451437GDF5_HUMAN211-5012911A:15-119105

(-) 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:105
 aligned with GDF5_HUMAN | P43026 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:105
                                   406       416       426       436       446       456       466       476       486       496     
           GDF5_HUMAN   397 KARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDSANNVVYKQYEDMVVESCGCR 501
               SCOP domains d2bhka_ A: automated matches                                                                              SCOP domains
               CATH domains 2bhkA00 A:15-119 Cystine-knot cytokines                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee.hhh.....eee..eee..eee.......hhhhh.hhhhhhhhhhhhhh........eeeeeeeeeeeeee.....eeeeeeeeeeeeeeee. Sec.struct. author
             SAPs(SNPs) (1) --CY-------------R---------------------T-LTLP---K-----------------------------N----------M----K---------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------T-------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------TGF_BETA_1      -------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.4  PDB: A:15-119 UniProt: 211-501 [INCOMPLETE]                                                     Transcript 1
                 2bhk A  15 KARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDSANNVVYKQYEDMVVESCGCR 119
                                    24        34        44        54        64        74        84        94       104       114     

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BHK)

(-) Gene Ontology  (37, 37)

Asymmetric Unit(hide GO term definitions)
Chain A   (GDF5_HUMAN | P43026)
molecular function
    GO:0036122    BMP binding    Interacting selectively and non-covalently with a member of the bone morphogenetic protein (BMP) family.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0005160    transforming growth factor beta receptor binding    Interacting selectively and non-covalently with the transforming growth factor beta receptor.
biological process
    GO:0007184    SMAD protein import into nucleus    The directed movement of a SMAD proteins from the cytoplasm into the nucleus. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0060395    SMAD protein signal transduction    The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.
    GO:0051216    cartilage development    The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0048468    cell development    The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0060591    chondroblast differentiation    The process in which a mesenchymal cell, acquires specialized structural and/or functional features of a chondroblast. Differentiation includes the processes involved in commitment of a cell to a chondroblast fate. A chondroblast is a precursor cell to chondrocytes.
    GO:0002062    chondrocyte differentiation    The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage.
    GO:0030326    embryonic limb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping.
    GO:0035136    forelimb morphogenesis    The process in which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0035137    hindlimb morphogenesis    The process in which the anatomical structures of the hindlimb are generated and organized.
    GO:0032331    negative regulation of chondrocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of chondrocyte differentiation.
    GO:0050680    negative regulation of epithelial cell proliferation    Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation.
    GO:2001054    negative regulation of mesenchymal cell apoptotic process    Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell apoptotic process.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0030513    positive regulation of BMP signaling pathway    Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity.
    GO:0032332    positive regulation of chondrocyte differentiation    Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation.
    GO:0098779    positive regulation of macromitophagy in response to mitochondrial depolarization    The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
    GO:0045666    positive regulation of neuron differentiation    Any process that activates or increases the frequency, rate or extent of neuron differentiation.
    GO:0010862    positive regulation of pathway-restricted SMAD protein phosphorylation    Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0043408    regulation of MAPK cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0040014    regulation of multicellular organism growth    Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0007178    transmembrane receptor protein serine/threonine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses serine/threonine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    IPA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:38 - Pro A:39   [ RasMol ]  
    Phe A:53 - Pro A:54   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2bhk
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GDF5_HUMAN | P43026
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  113100
    Disease InformationOMIM
  200700
    Disease InformationOMIM
  228900
    Disease InformationOMIM
  610017
    Disease InformationOMIM
  615072
    Disease InformationOMIM
  615298
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  GDF5_HUMAN | P43026
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GDF5_HUMAN | P430261waq 3evs 3qb4 5hk5

(-) Related Entries Specified in the PDB File

1waq CRYSTAL STRUCTURE OF HUMAN GROWTH AND DIFFERENTIATION FACTOR 5 (GDF- 5)