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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF VACCINIA-RELATED KINASE 2
 
Authors :  G. Bunkoczi, J. Eswaran, C. Cooper, O. Fedorov, T. Keates, P. Rellos, E. P. Savitsky, E. Ugochukwu, F. Von Delft, C. H. Arrowsmith, A. Edwards M. Sundstrom, J. Weigelt, S. Knapp
Date :  13 Jul 07  (Deposition) - 21 Aug 07  (Release) - 30 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Atp-Binding, Membrane, Nucleotide-Binding, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. D. Scheeff, J. Eswaran, G. Bunkoczi, S. Knapp, G. Manning
Structure Of The Pseudokinase Vrk3 Reveals A Degraded Catalytic Site, A Highly Conserved Kinase Fold, And A Putative Regulatory Binding Site.
Structure V. 17 128 2009
PubMed-ID: 19141289  |  Reference-DOI: 10.1016/J.STR.2008.10.018

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE VRK2
    ChainsA, B
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentKINASE DOMAIN, RESIDUES 14-335
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVACCINIA RELATED PROTEIN KINASE 2

 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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MG1Ligand/IonMAGNESIUM ION
3SIN1Ligand/IonSUCCINIC ACID
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3SIN1Ligand/IonSUCCINIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3SIN-1Ligand/IonSUCCINIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:207 , HOH A:1084 , HOH A:1085 , ARG B:207 , HOH B:1094 , HOH B:1096BINDING SITE FOR RESIDUE MG A1331
2AC2SOFTWAREARG A:117 , HOH A:1167 , HOH A:1168 , HOH A:1169 , MET B:24 , LEU B:74 , GLN B:78 , SER B:106 , GLY B:107 , ARG B:117BINDING SITE FOR RESIDUE SIN A1332
3AC3SOFTWARESER A:297 , CYS B:245 , TRP B:278 , PRO B:280BINDING SITE FOR RESIDUE EDO B1331
4AC4SOFTWARECYS A:245 , TRP A:278 , PRO A:280 , SER B:297 , HOH B:1150BINDING SITE FOR RESIDUE EDO A1333
5AC5SOFTWAREARG A:79 , ASN A:160 , GLU A:161 , GLU B:25 , ARG B:92BINDING SITE FOR RESIDUE EDO A1334

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V62)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:271 -Pro A:272
2Leu B:271 -Pro B:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041293N50DVRK2_HUMANPolymorphism34130684A/BN50D
2UniProtVAR_041294I157MVRK2_HUMANPolymorphism35966666A/BI157M
3UniProtVAR_017095I167VVRK2_HUMANPolymorphism1051061A/BI167V
4UniProtVAR_051681N211SVRK2_HUMANPolymorphism36081172A/BN211S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041293N50DVRK2_HUMANPolymorphism34130684AN50D
2UniProtVAR_041294I157MVRK2_HUMANPolymorphism35966666AI157M
3UniProtVAR_017095I167VVRK2_HUMANPolymorphism1051061AI167V
4UniProtVAR_051681N211SVRK2_HUMANPolymorphism36081172AN211S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041293N50DVRK2_HUMANPolymorphism34130684BN50D
2UniProtVAR_041294I157MVRK2_HUMANPolymorphism35966666BI157M
3UniProtVAR_017095I167VVRK2_HUMANPolymorphism1051061BI167V
4UniProtVAR_051681N211SVRK2_HUMANPolymorphism36081172BN211S

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.VRK2_HUMAN162-174
 
  2A:162-174
B:162-174
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.VRK2_HUMAN162-174
 
  1A:162-174
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.VRK2_HUMAN162-174
 
  1-
B:162-174

(-) Exons   (10, 20)

Asymmetric Unit (10, 20)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.7eENST000003401577eENSE00001824250chr2:58273826-58274003178VRK2_HUMAN-00--
1.10aENST0000034015710aENSE00002191870chr2:58275962-58276102141VRK2_HUMAN1-46462A:15-46 (gaps)
B:15-46 (gaps)
32
32
1.12ENST0000034015712ENSE00001785496chr2:58311224-5831127350VRK2_HUMAN46-62172A:46-62
B:46-62
17
17
1.13bENST0000034015713bENSE00001717868chr2:58312016-5831208570VRK2_HUMAN63-86242A:63-86 (gaps)
B:63-86 (gaps)
24
24
1.14ENST0000034015714ENSE00001798023chr2:58313474-5831356188VRK2_HUMAN86-115302A:86-115
B:86-115
30
30
1.15ENST0000034015715ENSE00001636501chr2:58315476-58315581106VRK2_HUMAN115-150362A:115-150
B:115-150
36
36
1.16ENST0000034015716ENSE00001609668chr2:58316766-5831685893VRK2_HUMAN151-181312A:151-181
B:151-181
31
31
1.17ENST0000034015717ENSE00001659851chr2:58350236-58350368133VRK2_HUMAN182-226452A:182-226
B:182-226
45
45
1.18ENST0000034015718ENSE00001765647chr2:58358943-58359063121VRK2_HUMAN226-266412A:226-266
B:226-266
41
41
1.19ENST0000034015719ENSE00001739841chr2:58362276-5836233459VRK2_HUMAN266-286212A:266-286
B:266-286
21
21
1.20ENST0000034015720ENSE00001679660chr2:58366801-58366967167VRK2_HUMAN286-341562A:286-330
B:286-330
45
45
1.21aENST0000034015721aENSE00001716305chr2:58373451-58373609159VRK2_HUMAN342-394530--
1.24dENST0000034015724dENSE00001872381chr2:58386484-58387006523VRK2_HUMAN395-5081140--

(-) 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:309
 aligned with VRK2_HUMAN | Q86Y07 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:316
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324      
           VRK2_HUMAN    15 FPEGKVLDDMEGNQWVLGKKIGSGGFGLIYLAFPTNKPEKDARHVVKVEYQENGPLFSELKFYQRVAKKDCIKKWIERKQLDYLGIPLFYGSGLTEFKGRSYRFMVMERLGIDLQKISGQNGTFKKSTVLQLGIRMLDVLEYIHENEYVHGDIKAANLLLGYKNPDQVYLADYGLSYRYCPNGNHKQYQENPRKGHNGTIEFTSLDAHKGVALSRRSDVEILGYCMLRWLCGKLPWEQNLKDPVAVQTAKTNLLDELPQSVLKWAPSGSSCCEIAQFLVCAHSLAYDEKPNYQALKKILNPHGIPLGPLDFSTKGQ 330
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.....eeeeeee.------.eeeeee...hhhhh.eeeeeee..-hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeee....eeeeeeee.eeeehhhhh.hhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee......eee......ee.hhhhh......hhhhh........hhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -----------------------------------D----------------------------------------------------------------------------------------------------------M---------V-------------------------------------------S----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.10a  PDB: A:15-46 (gaps) ----------------Exon 1.13b              ----------------------------Exon 1.15  PDB: A:115-150           Exon 1.16  PDB: A:151-181      Exon 1.17  PDB: A:182-226 UniProt: 182-226   ---------------------------------------Exon 1.19            -------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.12        -----------------------Exon 1.14  PDB: A:86-115      --------------------------------------------------------------------------------------------------------------Exon 1.18  PDB: A:226-266                -------------------Exon 1.20  PDB: A:286-330 UniProt: 286-341    Transcript 1 (2)
                 2v62 A  15 FPEGKVLDDMEGNQWVLGKKI------LIYLAFPTNKPEKDARHVVKVEYQE-GPLFSELKFYQRVAKKDCIKKWIERKQLDYLGIPLFYGSGLTEFKGRSYRFMVMERLGIDLQKISGQNGTFKKSTVLQLGIRMLDVLEYIHENEYVHGDIKAANLLLGYKNPDQVYLADYGLSYRYCPNGNHKQYQENPRKGHNGTIEFTSLDAHKGVALSRRSDVEILGYCMLRWLCGKLPWEQNLKDPVAVQTAKTNLLDELPQSVLKWAPSGSSCCEIAQFLVCAHSLAYDEKPNYQALKKILNPHGIPLGPLDFSTKGQ 330
                                    24        34|      |44        54        64 | |    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324      
                                               35     42                      66 |                                                                                                                                                                                                                                                                      
                                                                                68                                                                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with VRK2_HUMAN | Q86Y07 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:316
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324      
           VRK2_HUMAN    15 FPEGKVLDDMEGNQWVLGKKIGSGGFGLIYLAFPTNKPEKDARHVVKVEYQENGPLFSELKFYQRVAKKDCIKKWIERKQLDYLGIPLFYGSGLTEFKGRSYRFMVMERLGIDLQKISGQNGTFKKSTVLQLGIRMLDVLEYIHENEYVHGDIKAANLLLGYKNPDQVYLADYGLSYRYCPNGNHKQYQENPRKGHNGTIEFTSLDAHKGVALSRRSDVEILGYCMLRWLCGKLPWEQNLKDPVAVQTAKTNLLDELPQSVLKWAPSGSSCCEIAQFLVCAHSLAYDEKPNYQALKKILNPHGIPLGPLDFSTKGQ 330
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------Pkinase     -2v62B01 B:29-312                                                                                                                                                                                                                                                               ------------------ Pfam domains (1)
           Pfam domains (2) --------------Pkinase     -2v62B02 B:29-312                                                                                                                                                                                                                                                               ------------------ Pfam domains (2)
         Sec.struct. author .....eee.....eeeeeeee-----.eeeeeee...hhhhh.eeeee....-hhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeeee....eeeeeeee.eeee......hhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee......eee......ee.hhhhh......hhhhh........hhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhh.......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -----------------------------------D----------------------------------------------------------------------------------------------------------M---------V-------------------------------------------S----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.10a  PDB: B:15-46 (gaps) ----------------Exon 1.13b              ----------------------------Exon 1.15  PDB: B:115-150           Exon 1.16  PDB: B:151-181      Exon 1.17  PDB: B:182-226 UniProt: 182-226   ---------------------------------------Exon 1.19            -------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.12        -----------------------Exon 1.14  PDB: B:86-115      --------------------------------------------------------------------------------------------------------------Exon 1.18  PDB: B:226-266                -------------------Exon 1.20  PDB: B:286-330 UniProt: 286-341    Transcript 1 (2)
                 2v62 B  15 FPEGKVLDDMEGNQWVLGKKI-----GLIYLAFPTNKPEKDARHVVKVEYQE-GPLFSELKFYQRVAKKDCIKKWIERKQLDYLGIPLFYGSGLTEFKGRSYRFMVMERLGIDLQKISGQNGTFKKSTVLQLGIRMLDVLEYIHENEYVHGDIKAANLLLGYKNPDQVYLADYGLSYRYCPNGNHKQYQENPRKGHNGTIEFTSLDAHKGVALSRRSDVEILGYCMLRWLCGKLPWEQNLKDPVAVQTAKTNLLDELPQSVLKWAPSGSSCCEIAQFLVCAHSLAYDEKPNYQALKKILNPHGIPLGPLDFSTKGQ 330
                                    24        34|     | 44        54        64 | |    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324      
                                               35    41                       66 |                                                                                                                                                                                                                                                                      
                                                                                68                                                                                                                                                                                                                                                                      

   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 2V62)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V62)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (VRK2_HUMAN | Q86Y07)
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: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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine 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.
biological process
    GO:0034599    cellular response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    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: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:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:2000659    regulation of interleukin-1-mediated signaling pathway    Any process that modulates the frequency, rate or extent of interleukin-1-mediated signaling pathway.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SIN  [ 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
    Leu A:271 - Pro A:272   [ RasMol ]  
    Leu B:271 - Pro B:272   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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
  2v62
    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
  VRK2_HUMAN | Q86Y07
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    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
  VRK2_HUMAN | Q86Y07
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        VRK2_HUMAN | Q86Y075uu1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2V62)