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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TYRO3-D1D2
 
Authors :  C. Heiring, B. Dahlback, Y. A. Muller
Date :  14 Nov 03  (Deposition) - 23 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Axl/Tyro3 Family, Cellular Adhesion, Ligand-Independent Dimerization, Mutational Analysis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Heiring, B. Dahlback, Y. A. Muller
Ligand Recognition And Homophilic Interactions In Tyro3: Structural Insights Into The Axl/Tyro3 Receptor Tyrosine Kinase Family.
J. Biol. Chem. V. 279 6952 2004
PubMed-ID: 14623883  |  Reference-DOI: 10.1074/JBC.M311750200

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE RECEPTOR TYRO3
    ChainsA, B
    EC Number2.7.1.112
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A+
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL IG-DOMAIN
    GeneTYRO3, RSE, SKY, DTK, BYK
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTYROSINE-PROTEIN KINASE RSE, TYROSINE-PROTEIN KINASE SKY, TYROSINE-PROTEIN KINASE DTK, PROTEIN-TYROSINE KINASE BYK

 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  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MSE4Mod. Amino AcidSELENOMETHIONINE
4ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MSE2Mod. Amino AcidSELENOMETHIONINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MSE2Mod. Amino AcidSELENOMETHIONINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:166 , ACT A:302 , HOH A:423 , HIS B:166BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREHIS A:166 , ASN A:167 , LEU A:168 , ZN A:301 , HOH A:363 , HIS B:166BINDING SITE FOR RESIDUE ACT A 302
3AC3SOFTWAREARG A:74 , THR A:176BINDING SITE FOR RESIDUE ACT A 303
4AC4SOFTWAREARG B:74 , TRP B:76 , THR B:176 , EPE B:306 , HOH B:342BINDING SITE FOR RESIDUE ACT B 304
5AC5SOFTWAREASP A:107 , LEU A:108 , HIS A:180 , ASP B:107 , LEU B:108 , ALA B:109 , HIS B:180 , HOH B:419BINDING SITE FOR RESIDUE ACT A 305
6AC6SOFTWARETRP B:76 , ILE B:87 , SER B:88 , ACT B:304 , HOH B:388BINDING SITE FOR RESIDUE EPE B 306

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:24 -A:77
2A:120 -A:163
3B:24 -B:77
4B:120 -B:163

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Gly A:124 -Pro A:125
2Pro A:125 -Pro A:126
3Glu A:127 -Pro A:128
4Gly A:142 -Pro A:143
5Ser A:146 -Pro A:147
6Gly B:124 -Pro B:125
7Pro B:125 -Pro B:126
8Glu B:127 -Pro B:128
9Gly B:142 -Pro B:143
10Ser B:146 -Pro B:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RHF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RHF)

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002637981ENSE00001152512chr15:41851232-41851579348TYRO3_HUMAN1-42420--
1.2ENST000002637982ENSE00001106734chr15:41853325-41853508184TYRO3_HUMAN42-103622A:7-63
B:7-63
57
57
1.3ENST000002637983ENSE00000586489chr15:41853737-41853837101TYRO3_HUMAN103-137352A:63-97
B:63-97
35
35
1.4ENST000002637984ENSE00000676763chr15:41854746-41854916171TYRO3_HUMAN137-194582A:97-154
B:97-154
58
58
1.5ENST000002637985ENSE00000586496chr15:41856382-4185646887TYRO3_HUMAN194-223302A:154-182
B:154-182
29
29
1.6ENST000002637986ENSE00000676767chr15:41857224-41857339116TYRO3_HUMAN223-261390--
1.7ENST000002637987ENSE00000586427chr15:41859558-41859735178TYRO3_HUMAN262-321600--
1.8ENST000002637988ENSE00000676806chr15:41860415-41860560146TYRO3_HUMAN321-369490--
1.9ENST000002637989ENSE00000586436chr15:41861076-41861220145TYRO3_HUMAN370-418490--
1.10ENST0000026379810ENSE00000676821chr15:41862225-41862354130TYRO3_HUMAN418-461440--
1.11ENST0000026379811ENSE00000586447chr15:41862438-41862538101TYRO3_HUMAN461-495350--
1.12ENST0000026379812ENSE00000586453chr15:41862802-4186289796TYRO3_HUMAN495-527330--
1.13ENST0000026379813ENSE00000676824chr15:41863236-4186331681TYRO3_HUMAN527-554280--
1.14ENST0000026379814ENSE00000586464chr15:41863793-4186388593TYRO3_HUMAN554-585320--
1.15ENST0000026379815ENSE00000676826chr15:41864641-41864762122TYRO3_HUMAN585-625410--
1.16ENST0000026379816ENSE00000586471chr15:41865200-41865309110TYRO3_HUMAN626-662370--
1.17ENST0000026379817ENSE00000884066chr15:41865506-41865665160TYRO3_HUMAN662-715540--
1.18ENST0000026379818ENSE00000676867chr15:41865877-41866013137TYRO3_HUMAN716-761460--
1.19ENST0000026379819ENSE00001152503chr15:41870084-418715361453TYRO3_HUMAN761-8901300--

(-) 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:176
 aligned with TYRO3_HUMAN | Q06418 from UniProtKB/Swiss-Prot  Length:890

    Alignment length:176
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216      
          TYRO3_HUMAN    47 GAPVKLTVSQGQPVKLNCSVEGMEEPDIQWVKDGAVVQNLDQLYIPVSEQHWIGFLSLKSVERSDAGRYWCQVEDGGETEISQPVWLTVEGVPFFTVEPKDLAVPPNAPFQLSCEAVGPPEPVTIVWWRGTTKIGGPAPSPSVLNVTGVTQSTMFSCEAHNLKGLASSRTATVHLQ 222
               SCOP domains d1rhfa1 A:7-97 Tyrosine-protein kinase receptor tyro3, N-terminal domain                   d1rhfa2 A:98-182 Tyrosine-protein kinase receptor tyro3, second domain                SCOP domains
               CATH domains 1rhfA01 A:7-97 Immunoglobulins                                                             1rhfA02 A:98-182 Immunoglobulins                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eeeeeeee......eeeee..ee....eeeeeeee..eeeeeeee...hhhhheeeeeee......ee...eeeeee...eeee....eee.....eeeeeeee......eeeeee..ee....ee..eeeee......eeeeeeeee..eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:7-63 UniProt: 42-103 [INCOMPLETE]       ---------------------------------Exon 1.4  PDB: A:97-154 UniProt: 137-194                  ---------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.3  PDB: A:63-97             --------------------------------------------------------Exon 1.5  PDB: A:154-182      Transcript 1 (2)
                 1rhf A   7 GAPVKLTVSQGQPVKLNCSVEGmEEPDIQWVKDGAVVQNLDQLYIPVSEQHWIGFLSLKSVERSDAGRYWCQVEDGGETEISQPVWLTVEGVPFFTVEPKDLAVPPNAPFQLSCEAVGPPEPVTIVWWRGTTKIGGPAPSPSVLNVTGVTQSTmFSCEAHNLKGLASSRTATVHLQ 182
                                    16        26  |     36        46        56        66        76        86        96       106       116       126       136       146       156   |   166       176      
                                                 29-MSE                                                                                                                            160-MSE                  

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with TYRO3_HUMAN | Q06418 from UniProtKB/Swiss-Prot  Length:890

    Alignment length:176
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216      
          TYRO3_HUMAN    47 GAPVKLTVSQGQPVKLNCSVEGMEEPDIQWVKDGAVVQNLDQLYIPVSEQHWIGFLSLKSVERSDAGRYWCQVEDGGETEISQPVWLTVEGVPFFTVEPKDLAVPPNAPFQLSCEAVGPPEPVTIVWWRGTTKIGGPAPSPSVLNVTGVTQSTMFSCEAHNLKGLASSRTATVHLQ 222
               SCOP domains d1rhfb1 B:7-97 Tyrosine-protein kinase receptor tyro3, N-terminal domain                   d1rhfb2 B:98-182 Tyrosine-protein kinase receptor tyro3, second domain                SCOP domains
               CATH domains 1rhfB01 B:7-97 Immunoglobulins                                                             1rhfB02 B:98-182 Immunoglobulins                                                      CATH domains
           Pfam domains (1) I-set-1rhfB01 B:7-95                                                                     ------Ig_3-1rhfB03 B:102-167                                            --------------- Pfam domains (1)
           Pfam domains (2) I-set-1rhfB02 B:7-95                                                                     ------Ig_3-1rhfB04 B:102-167                                            --------------- Pfam domains (2)
         Sec.struct. author ...eeeeee....eeeeeeee......eeeee..ee.....eeeeeee..eeeeeeee...hhhhheeeeeee......ee...eeeeee...eeee....eee.....eeeeeeee......eeeeee..ee....ee..eeeee......eeeeeeeee..eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:7-63 UniProt: 42-103 [INCOMPLETE]       ---------------------------------Exon 1.4  PDB: B:97-154 UniProt: 137-194                  ---------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.3  PDB: B:63-97             --------------------------------------------------------Exon 1.5  PDB: B:154-182      Transcript 1 (2)
                 1rhf B   7 GAPVKLTVSQGQPVKLNCSVEGmEEPDIQWVKDGAVVQNLDQLYIPVSEQHWIGFLSLKSVERSDAGRYWCQVEDGGETEISQPVWLTVEGVPFFTVEPKDLAVPPNAPFQLSCEAVGPPEPVTIVWWRGTTKIGGPAPSPSVLNVTGVTQSTmFSCEAHNLKGLASSRTATVHLQ 182
                                    16        26  |     36        46        56        66        76        86        96       106       116       126       136       146       156   |   166       176      
                                                 29-MSE                                                                                                                            160-MSE                  

   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 Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (46, 46)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TYRO3_HUMAN | Q06418)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0043548    phosphatidylinositol 3-kinase binding    Interacting selectively and non-covalently with a phosphatidylinositol 3-kinase, any enzyme that catalyzes the addition of a phosphate group to an inositol lipid at the 3' position of the inositol ring.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0004716    signal transducer, downstream of receptor, with protein tyrosine kinase activity    Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0004714    transmembrane receptor protein tyrosine kinase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
    GO:0001618    virus receptor activity    Combining with a virus component and mediating entry of the virus into the cell.
biological process
    GO:0043277    apoptotic cell clearance    The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0021885    forebrain cell migration    The orderly movement of a cell from one site to another at least one of which is located in the forebrain.
    GO:0001779    natural killer cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a natural killer cell.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0045824    negative regulation of innate immune response    Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response.
    GO:0051250    negative regulation of lymphocyte activation    Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte activation.
    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:0034122    negative regulation of toll-like receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor signaling pathway.
    GO:0070050    neuron cellular homeostasis    The cellular homeostatic process that preserves a neuron in a stable, differentiated functional and structural state.
    GO:0042698    ovulation cycle    The type of sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0014065    phosphatidylinositol 3-kinase signaling    A series of reactions within the signal-receiving cell, mediated by the intracellular phosphatidylinositol 3-kinase (PI3K). Many cell surface receptor linked signaling pathways signal through PI3K to regulate numerous cellular functions.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0070527    platelet aggregation    The adhesion of one platelet to one or more other platelets via adhesion molecules.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0043491    protein kinase B signaling    A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase B (also called AKT), which occurs as a result of a single trigger reaction or compound.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0032940    secretion by cell    The controlled release of a substance by a cell.
    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.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0034446    substrate adhesion-dependent cell spreading    The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate.
    GO:0060068    vagina development    The reproductive developmental process whose specific outcome is the progression of the vagina over time, from its formation to the mature structure.
    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.
cellular component
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0005887    integral component of plasma membrane    The component of the plasma 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:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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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