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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE ERK2 COMPLEXED WITH EK5
 
Authors :  Y. N. Kang, J. A. Stuckey, X. Xie
Date :  29 Jun 12  (Deposition) - 29 Aug 12  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. N. Kang, J. A. Stuckey, X. Xie
Crystal Structure Of The Erk2 Complexed With Ek5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 1
    Chains: A
    EC Number: 2.7.11.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ERK2, MAPK1, PRKM1, PRKM2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: HUMAN
    Synonym: MAP KINASE 1, MAPK 1, ERT1, EXTRACELLULAR SIGNAL-REGULATED KINASE 2, ERK-2, MAP KINASE ISOFORM P42, P42-MAPK, MITOGEN-ACTIVATED PROTEIN KINASE 2, MAP KINASE 2, MAPK 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1CME1Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3EK51Ligand/Ion4-[4-(3-CHLOROPHENYL)-1H-PYRAZOL-5-YL]-N-(2,3-DIHYDRO-1-BENZOFURAN-5-YLMETHYL)-1H-PYRROLE-2-CARBOXAMIDE
4GOL3Ligand/IonGLYCEROL
5SO42Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:29 , GLY A:30 , GLU A:31 , GLY A:32 , GLY A:35 , VAL A:37 , ALA A:50 , LYS A:52 , ILE A:82 , GLN A:103 , ASP A:104 , MET A:106 , ASP A:109 , LEU A:154 , HOH A:658 , HOH A:674BINDING SITE FOR RESIDUE EK5 A 401
02AC2SOFTWAREARG A:189 , ARG A:192 , TYR A:231 , HOH A:580 , HOH A:611BINDING SITE FOR RESIDUE SO4 A 402
03AC3SOFTWARETHR A:61 , ARG A:65 , LEU A:168 , ARG A:170 , VAL A:186BINDING SITE FOR RESIDUE SO4 A 403
04AC4SOFTWAREGLU A:79 , ASN A:80 , TYR A:126 , GLN A:130 , ARG A:133 , ASP A:160 , HOH A:519 , HOH A:550BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWAREHIS A:297 , LYS A:298 , ARG A:299 , GLN A:304 , HOH A:577BINDING SITE FOR RESIDUE EDO A 405
06AC6SOFTWARELYS A:149 , SER A:151 , HOH A:583BINDING SITE FOR RESIDUE EDO A 406
07AC7SOFTWARELYS A:115 , HIS A:118 , ASN A:222BINDING SITE FOR RESIDUE EDO A 407
08AC8SOFTWAREPRO A:309 , TYR A:310BINDING SITE FOR RESIDUE EDO A 408
09AC9SOFTWAREALA A:280 , SER A:282 , GLU A:343BINDING SITE FOR RESIDUE EDO A 409
10BC1SOFTWAREASP A:18 , ARG A:89 , ALA A:90 , GLN A:95 , MET A:96 , LYS A:97 , ASP A:98 , HIS A:267BINDING SITE FOR RESIDUE GOL A 410
11BC2SOFTWARETYR A:314BINDING SITE FOR RESIDUE GOL A 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FV2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:20 -Pro A:21

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FV2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FV2)

(-) Exons   (0, 0)

(no "Exon" information available for 4FV2)

(-) 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:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4fv2a_ A: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeeee...eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhh.........eee..........eeeee....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.hhhhh..........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhh......hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhh...hhhhh..............hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fv2 A   9 PEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTcDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFELDDLPKEKLKELIFEETARFQPG 355
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158|      168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328||     340       350     
                                                                                                                                                                                159-CME                                                                                                                                                                   329|                       
                                                                                                                                                                                                                                                                                                                                                           332
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FV2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FV2)

(-) Gene Ontology  (107, 107)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EK5  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:20 - Pro A:21   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4fv2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MK01_HUMAN | P28482
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.24
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MK01_HUMAN | P28482
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MK01_HUMAN | P28482: 1pme 1tvo 1wzy 2ojg 2oji 2ojj 2y9q 3d42 3d44 3i5z 3i60 3sa0 3tei 3w55 4fmq 4fux 4fuy 4fv0 4fv1 4fv3 4fv4 4fv5 4fv6 4fv7 4fv8 4fv9 4g6n 4g6o 4h3p 4h3q 4iz5 4iz7 4iza 4n0s 4nif 4o6e 4qp1 4qp2 4qp3 4qp4 4qp6 4qp7 4qp8 4qp9 4qpa 4qta 4qte 4xj0 4zxt 4zzm 4zzn 4zzo 5ax3 5bue 5bui 5buj 5bvd 5bve 5bvf 5k4i 5lcj 5lck 5ngu 5nhf 5nhh 5nhj 5nhl 5nho 5nhp 5nhv

(-) Related Entries Specified in the PDB File

4fux CRYSTAL STRUCTURE OF THE ERK2 COMPLEXED WITH E75
4fuy CRYSTAL STRUCTURE OF THE ERK2 COMPLEXED WITH EK2
4fv0 CRYSTAL STRUCTURE OF THE ERK2 COMPLEXED WITH EK3
4fv1 CRYSTAL STRUCTURE OF THE ERK2 COMPLEXED WITH EK4
4fv3 CRYSTAL STRUCTURE OF THE ERK2 COMPLEXED WITH EK6
4fv4 CRYSTAL STRUCTURE OF THE ERK2 COMPLEXED WITH EK7
4fv5 CRYSTAL STRUCTURE OF THE ERK2 COMPLEXED WITH EK9
4fv6 CRYSTAL STRUCTURE OF THE ERK2 COMPLEXED WITH E57
4fv7 CRYSTAL STRUCTURE OF THE ERK2 COMPLEXED WITH E94
4fv8 CRYSTAL STRUCTURE OF THE ERK2 COMPLEXED WITH E63
4fv9 CRYSTAL STRUCTURE OF THE ERK2 COMPLEXED WITH E71