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(-) Description

Title :  CRYSTAL STRUCTURE OF EPHB4 IN COMPLEX WITH STAUROSPORINE
 
Authors :  J. E. Debreczeni, R. Overman, C. Truman, M. Mcalister, T. K. Attwood
Date :  07 Dec 12  (Deposition) - 25 Dec 13  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. C. Overman, J. E. Debreczeni, C. M. Truman, M. S. Mcalister, T. K. Attwood
Completing The Structural Family Portrait Of The Human Ephb Tyrosine Kinase Domains
Protein Sci. V. 23 627 2014
PubMed-ID: 24677421  |  Reference-DOI: 10.1002/PRO.2445

(-) Compounds

Molecule 1 - EPHRIN TYPE-B RECEPTOR 4
    ChainsA, B
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantSTAR
    Expression System VectorPET28
    Expression System Vector TypePLASMID
    FragmentKINASE DOMAIN, RESIDUES 598-892
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEPHB4, HEPATOMA TRANSMEMBRANE KINASE, TYROSINE-PROTEIN KINASE TYRO11

 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, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
2SO44Ligand/IonSULFATE ION
3STU2Ligand/IonSTAUROSPORINE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
2SO42Ligand/IonSULFATE ION
3STU1Ligand/IonSTAUROSPORINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1PTR-1Mod. Amino AcidO-PHOSPHOTYROSINE
2SO42Ligand/IonSULFATE ION
3STU1Ligand/IonSTAUROSPORINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:621 , GLY A:622 , ALA A:645 , LYS A:647 , GLU A:664 , THR A:693 , GLU A:694 , PHE A:695 , MET A:696 , GLY A:699 , ARG A:744 , LEU A:747 , SER A:757BINDING SITE FOR RESIDUE STU A 1889
2AC2SOFTWAREILE B:621 , GLY B:622 , ALA B:645 , GLU B:664 , THR B:693 , GLU B:694 , PHE B:695 , MET B:696 , GLY B:699 , ARG B:744 , LEU B:747 , SER B:757BINDING SITE FOR RESIDUE STU B 1888
3AC3SOFTWAREARG A:722 , ARG A:729BINDING SITE FOR RESIDUE SO4 A 1890
4AC4SOFTWAREARG B:722 , ARG B:729 , HOH B:2005BINDING SITE FOR RESIDUE SO4 B 1889
5AC5SOFTWARELYS A:876 , ARG A:879BINDING SITE FOR RESIDUE SO4 A 1891
6AC6SOFTWAREARG B:879 , ASN B:880BINDING SITE FOR RESIDUE SO4 B 1890

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZEW)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Met A:687 -Pro A:688
2Met B:687 -Pro B:688

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042186R678HEPHB4_HUMANPolymorphism55692440A/BR678H
2UniProtVAR_078063R739QEPHB4_HUMANDisease (HFASD)  ---A/BR739Q
3UniProtVAR_078064I782SEPHB4_HUMANDisease (HFASD)  ---A/BI782S
4UniProtVAR_042187A882TEPHB4_HUMANPolymorphism34918225A/BA882T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042186R678HEPHB4_HUMANPolymorphism55692440AR678H
2UniProtVAR_078063R739QEPHB4_HUMANDisease (HFASD)  ---AR739Q
3UniProtVAR_078064I782SEPHB4_HUMANDisease (HFASD)  ---AI782S
4UniProtVAR_042187A882TEPHB4_HUMANPolymorphism34918225AA882T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042186R678HEPHB4_HUMANPolymorphism55692440BR678H
2UniProtVAR_078063R739QEPHB4_HUMANDisease (HFASD)  ---BR739Q
3UniProtVAR_078064I782SEPHB4_HUMANDisease (HFASD)  ---BI782S
4UniProtVAR_042187A882TEPHB4_HUMANPolymorphism34918225BA882T

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.EPHB4_HUMAN621-647
 
  2A:621-647
B:621-647
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.EPHB4_HUMAN736-748
 
  2A:736-748
B:736-748
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.EPHB4_HUMAN621-647
 
  1A:621-647
-
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.EPHB4_HUMAN736-748
 
  1A:736-748
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.EPHB4_HUMAN621-647
 
  1-
B:621-647
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.EPHB4_HUMAN736-748
 
  1-
B:736-748

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003581731bENSE00001868923chr7:100425121-100424601521EPHB4_HUMAN1-18180--
1.2bENST000003581732bENSE00000825052chr7:100421895-10042182571EPHB4_HUMAN18-41240--
1.3ENST000003581733ENSE00000825051chr7:100421553-100421266288EPHB4_HUMAN42-137960--
1.4ENST000003581734ENSE00000825050chr7:100420289-100419893397EPHB4_HUMAN138-2701330--
1.5bENST000003581735bENSE00000825049chr7:100417918-100417763156EPHB4_HUMAN270-322530--
1.6ENST000003581736ENSE00000825048chr7:100417511-100417179333EPHB4_HUMAN322-4331120--
1.7bENST000003581737bENSE00000710240chr7:100416266-100416142125EPHB4_HUMAN433-474420--
1.8cENST000003581738cENSE00001706820chr7:100414979-100414814166EPHB4_HUMAN475-530560--
1.9cENST000003581739cENSE00001665919chr7:100411643-100411541103EPHB4_HUMAN530-564350--
1.10ENST0000035817310ENSE00001787983chr7:100411338-10041127465EPHB4_HUMAN564-586230--
1.11bENST0000035817311bENSE00001754468chr7:100410830-100410717114EPHB4_HUMAN586-624392A:609-624
B:609-624
16
16
1.12ENST0000035817312ENSE00001631272chr7:100410616-100410369248EPHB4_HUMAN624-706832A:624-706 (gaps)
B:624-706 (gaps)
83
83
1.13aENST0000035817313aENSE00001753966chr7:100405202-100404987216EPHB4_HUMAN707-778722A:707-777 (gaps)
B:707-760
71
54
1.14aENST0000035817314aENSE00001623534chr7:100404191-100404042150EPHB4_HUMAN779-828502A:781-828
B:782-828
48
47
1.15ENST0000035817315ENSE00001783205chr7:100403316-100403123194EPHB4_HUMAN829-893652A:829-888
B:829-887
60
59
1.16ENST0000035817316ENSE00001649970chr7:100402943-100402788156EPHB4_HUMAN893-945530--
1.17bENST0000035817317bENSE00001639386chr7:100401212-1004001871026EPHB4_HUMAN945-987430--

(-) 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:270
 aligned with EPHB4_HUMAN | P54760 from UniProtKB/Swiss-Prot  Length:987

    Alignment length:280
                                   618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888
          EPHB4_HUMAN   609 EIDVSYVKIEEVIGAGEFGEVCRGRLKAPGKKESCVAIKTLKGGYTERQRREFLSEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRLNDGQFTVIQLVGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVSDFGLSRFLEENSSDPTYTSSLGGKIPIRWTAPEAIAFRKFTSASDAWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPPDCPTSLHQLMLDCWQKDRNARPRFPQVVSALDKMIRNPASLKIVA 888
               SCOP domains d3zewa_ A: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeeeeeee....eeeeeee.......eeeeeee.----hhhhhhhhhhhhhhhhh........eeeee......eeeee....eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.---.....ee..---..hhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------H------------------------------------------------------------Q------------------------------------------S---------------------------------------------------------------------------------------------------T------ SAPs(SNPs)
                    PROSITE ------------PROTEIN_KINASE_ATP         ----------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11b      ----------------------------------------------------------------------------------Exon 1.13a  PDB: A:707-777 (gaps) UniProt: 707-778 [INCOMPLETE]         Exon 1.14a  PDB: A:781-828 UniProt: 779-828       Exon 1.15  PDB: A:829-888 UniProt: 829-893 [INCOMPLETE]      Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.12  PDB: A:624-706 (gaps) UniProt: 624-706                                  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3zew A 609 EIDVSYVKIEEVIGAGEFGEVCRGRLKAPGKKESCVAIKTL----TERQRREFLSEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRLNDGQFTVIQLVGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVSDFGLSRFL---SSDPTyTSS---KIPIRWTAPEAIAFRKFTSASDAWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPPDCPTSLHQLMLDCWQKDRNARPRFPQVVSALDKMIRNPASLKIVA 888
                                   618       628       638       648|    | 658       668       678       688       698       708       718       728       738       748       758      |  -|    |  |-  |    788       798       808       818       828       838       848       858       868       878       888
                                                                  649  654                                                                                                            765 769    |  | 781                                                                                                           
                                                                                                                                                                                               774-PTR                                                                                                              
                                                                                                                                                                                                  777                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with EPHB4_HUMAN | P54760 from UniProtKB/Swiss-Prot  Length:987

    Alignment length:279
                                   618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878         
          EPHB4_HUMAN   609 EIDVSYVKIEEVIGAGEFGEVCRGRLKAPGKKESCVAIKTLKGGYTERQRREFLSEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRLNDGQFTVIQLVGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVSDFGLSRFLEENSSDPTYTSSLGGKIPIRWTAPEAIAFRKFTSASDAWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPPDCPTSLHQLMLDCWQKDRNARPRFPQVVSALDKMIRNPASLKIV 887
               SCOP domains d3zewb_ B: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeeeeeee....eeeeeee..--...eeeeeee.----hhhhhhhhhhhhhhhhh........eeeee......eeeee....eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee....---------------------.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------H------------------------------------------------------------Q------------------------------------------S---------------------------------------------------------------------------------------------------T----- SAPs(SNPs)
                    PROSITE ------------PROTEIN_KINASE_ATP         ----------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11b      ----------------------------------------------------------------------------------Exon 1.13a  PDB: B:707-760 UniProt: 707-778 [INCOMPLETE]                Exon 1.14a  PDB: B:782-828 UniProt: 779-828       Exon 1.15  PDB: B:829-887 UniProt: 829-893 [INCOMPLETE]     Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.12  PDB: B:624-706 (gaps) UniProt: 624-706                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3zew B 609 EIDVSYVKIEEVIGAGEFGEVCRGRLKA--KKESCVAIKTL----TERQRREFLSEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRLNDGQFTVIQLVGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVSDFG---------------------IPIRWTAPEAIAFRKFTSASDAWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPPDCPTSLHQLMLDCWQKDRNARPRFPQVVSALDKMIRNPASLKIV 887
                                   618       628       | -|      648|    | 658       668       678       688       698       708       718       728       738       748       758 |       -         -   |   788       798       808       818       828       838       848       858       868       878         
                                                     636  |       649  654                                                                                                       760                   782                                                                                                         
                                                        639                                                                                                                                                                                                                                                        

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZEW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZEW)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (EPHB4_HUMAN | P54760)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005003    ephrin receptor activity    Combining with an ephrin to initiate a change in cell activity.
    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: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: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: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.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    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:0002042    cell migration involved in sprouting angiogenesis    The orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels involved in sprouting angiogenesis.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    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: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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0007169    transmembrane receptor protein tyrosine 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 tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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: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: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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  EPHB4_HUMAN | P54760
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EPHB4_HUMAN | P547602bba 2e7h 2hle 2qkq 2vwu 2vwv 2vww 2vwx 2vwy 2vwz 2vx0 2vx1 2x9f 2xvd 2yn8 4aw5 4bb4

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3ZEW)