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(-) Description

Title :  NK1 FRAGMENT OF HUMAN HEPATOCYTE GROWTH FACTOR
 
Authors :  M. H. Ultsch, N. A. Lokker, P. J. Godowski, A. M. De Vos
Date :  10 Jun 98  (Deposition) - 04 Nov 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Heparin-Binding Domain, Kringle, C-Met Receptor Angonist/ Antagonist, Growth Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Ultsch, N. A. Lokker, P. J. Godowski, A. M. De Vos
Crystal Structure Of The Nk1 Fragment Of Human Hepatocyte Growth Factor At 2. 0 A Resolution.
Structure V. 6 1383 1998
PubMed-ID: 9817840  |  Reference-DOI: 10.1016/S0969-2126(98)00138-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEPATOCYTE GROWTH FACTOR
    Cellular LocationCYTOPLASM
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPF-NK1
    Expression System Strain27C7
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentNK1 FRAGMENT, HEPARIN BINDING DOMAIN PLUS C-MET BINDING DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsHEPES BUFFER MOLECULE BOUND IN KRINGLE BINDING POCKET
    SynonymNK1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:60 , LYS A:62 , ARG A:73 , ARG A:181 , HOH A:832BINDING SITE FOR RESIDUE SO4 A 5
2AC2SOFTWAREARG B:468 , GLY B:469 , ASP B:471 , GLN B:473 , HOH B:624 , HOH B:699 , HOH B:887BINDING SITE FOR RESIDUE SO4 B 6
3AC3SOFTWAREARG A:168 , GLY A:169 , LYS A:170 , ASP A:171 , HOH A:682 , HOH A:727BINDING SITE FOR RESIDUE SO4 A 7
4AC4SOFTWAREGLU A:183 , GLU A:184 , GLY A:185 , GLY A:186 , TRP A:188 , PHE A:190 , ARG A:197 , TYR A:198 , VAL A:200 , HOH A:710 , HOH A:724BINDING SITE FOR RESIDUE EPE A 1
5AC5SOFTWARESER B:461 , GLU B:483 , GLU B:484 , GLY B:485 , GLY B:486 , TRP B:488 , PHE B:490 , ARG B:497 , HOH B:603 , HOH B:717BINDING SITE FOR RESIDUE EPE B 2

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:70 -A:96
2A:74 -A:84
3A:128 -A:206
4A:149 -A:189
5A:177 -A:201
6B:370 -B:396
7B:374 -B:384
8B:428 -B:506
9B:449 -B:489
10B:477 -B:501

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:156 -Pro A:157
2Ile B:456 -Pro B:457

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014570S153IHGF_HUMANPolymorphism17566A
B
S153
453
I

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

(-) PROSITE Motifs  (3, 7)

Asymmetric/Biological Unit (3, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PANPS50948 PAN/Apple domain profile.HGF_HUMAN37-123
 
  2A:37-123
B:337-423
2KRINGLE_2PS50070 Kringle domain profile.HGF_HUMAN127-206
 
210-288
304-383
390-469
  3A:127-206
B:427-506
A:210-210
-
-
3KRINGLE_1PS00021 Kringle domain signature.HGF_HUMAN176-189
 
259-271
353-365
439-452
  2A:176-189
B:476-489
-
-
-

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002223902aENSE00001949645chr7:81399514-81399200315HGF_HUMAN1-30300--
1.3bENST000002223903bENSE00000698746chr7:81392188-81392023166HGF_HUMAN30-85562A:35-85
B:336-385
51
50
1.4bENST000002223904bENSE00001790262chr7:81388120-81388008113HGF_HUMAN85-123392A:85-123
B:385-423
39
39
1.5bENST000002223905bENSE00000698725chr7:81386619-81386505115HGF_HUMAN123-161392A:123-161
B:423-461
39
39
1.6aENST000002223906aENSE00000698723chr7:81381578-81381436143HGF_HUMAN161-209492A:161-209
B:461-509
49
49
1.7ENST000002223907ENSE00000698721chr7:81374436-81374316121HGF_HUMAN209-249412A:209-210
B:509-509
2
1
1.8ENST000002223908ENSE00000698671chr7:81372787-81372669119HGF_HUMAN249-289410--
1.10ENST0000022239010ENSE00000698668chr7:81359095-81358921175HGF_HUMAN289-347590--
1.11ENST0000022239011ENSE00000698665chr7:81355333-81355206128HGF_HUMAN347-390440--
1.12ENST0000022239012ENSE00000698663chr7:81350163-81350061103HGF_HUMAN390-424350--
1.13ENST0000022239013ENSE00000698662chr7:81346681-81346548134HGF_HUMAN424-469460--
1.14ENST0000022239014ENSE00000698661chr7:81340835-8134079739HGF_HUMAN469-482140--
1.15ENST0000022239015ENSE00000698660chr7:81339559-8133946397HGF_HUMAN482-514330--
1.16ENST0000022239016ENSE00000698659chr7:81336680-8133660675HGF_HUMAN514-539260--
1.17ENST0000022239017ENSE00000698658chr7:81335743-81335603141HGF_HUMAN539-586480--
1.18ENST0000022239018ENSE00000698657chr7:81335069-81334963107HGF_HUMAN586-622370--
1.19ENST0000022239019ENSE00000698655chr7:81334851-81334706146HGF_HUMAN622-670490--
1.20bENST0000022239020bENSE00001870741chr7:81332073-813283223752HGF_HUMAN671-728580--

(-) Sequences/Alignments

Asymmetric/Biological 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:176
 aligned with HGF_HUMAN | P14210 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:176
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204      
            HGF_HUMAN    35 RRNTIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEVE 210
               SCOP domains d1bhta1 A:35-126 Hepatocyte growth factor                                                   d1bhta2 A:127-210 NK1 fragment of hepatocyte growth factor                           SCOP domains
               CATH domains 1bhtA01 A:35-125 Hepatocyte Growth Factor                                                  1bhtA02 A:126-210 Plasminogen Kringle 4                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhheeeee.eeeee......eeeee...hhhhhhhhhh.........eeeee....eeeee........eeeee...eeeeeehhh.......................................hhh.....................eee.......eee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --PAN  PDB: A:37-123 UniProt: 37-123                                                     ---KRINGLE_2  PDB: A:127-206 UniProt: 127-206                                      ---K PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------KRINGLE_1     --------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3b  PDB: A:35-85 UniProt: 30-85 [INCOMPLETE]-------------------------------------Exon 1.5b  PDB: A:123-161              -----------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.4b  PDB: A:85-123               -------------------------------------Exon 1.6a  PDB: A:161-209 UniProt: 161-209       - Transcript 1 (2)
                 1bht A  35 RRNTIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEVE 210
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204      

Chain B from PDB  Type:PROTEIN  Length:174
 aligned with HGF_HUMAN | P14210 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:174
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205    
            HGF_HUMAN    36 RNTIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEV 209
               SCOP domains d1bhtb1 B:336-426 Hepatocyte growth factor                                                 d1bhtb2 B:427-509 NK1 fragment of hepatocyte growth factor                          SCOP domains
               CATH domains 1bhtB01 B:336-425 Hepatocyte Growth Factor                                                1bhtB02 B:426-509 Plasminogen Kringle 4                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhheeeee.eeee.......eeeee...hhhhhhhhh..........eeeee....eeeee.........eeee...eeeeeehhh.......................................hhh.....................eee.......eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------I-------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PAN  PDB: B:337-423 UniProt: 37-123                                                    ---KRINGLE_2  PDB: B:427-506 UniProt: 127-206                                      --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------KRINGLE_1     -------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3b  PDB: B:336-385 UniProt: 30-85          -------------------------------------Exon 1.5b  PDB: B:423-461              -----------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.4b  PDB: B:385-423              -------------------------------------Exon 1.6a  PDB: B:461-509 UniProt: 161-209        Transcript 1 (2)
                 1bht B 336 RNTIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEV 509
                                   345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505    

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (47, 47)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HGF_HUMAN | P14210)
molecular function
    GO:0042056    chemoattractant activity    Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    GO:0060326    cell chemotaxis    The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0035729    cellular response to hepatocyte growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hepatocyte growth factor stimulus.
    GO:0001837    epithelial to mesenchymal transition    A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
    GO:0048012    hepatocyte growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of the hepatocyte growth factor receptor binding to one of its physiological ligands.
    GO:0030212    hyaluronan metabolic process    The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0051450    myoblast proliferation    The multiplication or reproduction of myoblasts, resulting in the expansion of a myoblast cell population. 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:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0010507    negative regulation of autophagy    Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:1902042    negative regulation of extrinsic apoptotic signaling pathway via death domain receptors    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
    GO:1901299    negative regulation of hydrogen peroxide-mediated programmed cell death    Any process that stops, prevents or reduces the frequency, rate or extent of hydrogen peroxide-mediated programmed cell death.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0032715    negative regulation of interleukin-6 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production.
    GO:0033137    negative regulation of peptidyl-serine phosphorylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:0090201    negative regulation of release of cytochrome c from mitochondria    Any process that decreases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0050918    positive chemotaxis    The directed movement of a motile cell or organism towards a higher concentration of a chemical.
    GO:2000573    positive regulation of DNA biosynthetic process    Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0032733    positive regulation of interleukin-10 production    Any process that activates or increases the frequency, rate, or extent of interleukin-10 production.
    GO:0031643    positive regulation of myelination    Any process that activates or increases the frequency, rate or extent of the formation of a myelin sheath around nerve axons.
    GO:0070572    positive regulation of neuron projection regeneration    Any process that activates or increases the frequency, rate or extent of neuron projection regeneration, the regrowth of neuronal processes such as axons or dendrites following their loss or damage.
    GO:0045669    positive regulation of osteoblast differentiation    Any process that activates or increases the frequency, rate or extent of osteoblast differentiation.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0060665    regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling    Any process that modulates the rate, frequency, or extent of branching involved in salivary gland morphogenesis as a result of signals being generated by the mesenchyme and received and interpreted by the salivary gland epithelium.
    GO:1900744    regulation of p38MAPK cascade    Any process that modulates the frequency, rate or extent of p38MAPK cascade.
    GO:1902947    regulation of tau-protein kinase activity    Any process that modulates the frequency, rate or extent of tau-protein kinase activity.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HGF_HUMAN | P142101gmn 1gmo 1gp9 1nk1 1shy 1si5 2ced 2cee 2ceg 2hgf 2qj2 3hms 3hmt 3hn4 3mkp 3sp8 4d3c 4k3j 4o3t 4o3u 5coe 5cp9 5cs1 5cs3 5cs5 5cs9 5csq 5ct1 5ct2 5ct3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BHT)