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 3MB-PP1 BOUND TO ANALOG-SENSITIVE SRC KINASE
 
Authors :  M. S. Lopez, A. C. Dar, K. M. Shokat
Date :  27 Jun 13  (Deposition) - 07 Aug 13  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Kinase Domain, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Zhang, M. S. Lopez, A. C. Dar, E. Ladow, S. Finkbeiner, C. H. Yun, M. J. Eck, K. M. Shokat
Structure-Guided Inhibitor Design Expands The Scope Of Analog-Sensitive Kinase Technology.
Acs Chem. Biol. V. 8 1931 2013
PubMed-ID: 23841803  |  Reference-DOI: 10.1021/CB400376P

(-) Compounds

Molecule 1 - PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC
    Chains: A, B
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: KINASE DOMAIN (UNP RESIDUES 264-533)
    Gene: SRC
    Mutation: YES
    Organism Common: BANTAM,CHICKENS
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Synonym: PROTO-ONCOGENE C-SRC, PP60C-SRC, P60-SRC

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1VGG2Ligand/Ion1-TERT-BUTYL-3-(3-METHYLBENZYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-AMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1VGG1Ligand/Ion1-TERT-BUTYL-3-(3-METHYLBENZYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-AMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1VGG1Ligand/Ion1-TERT-BUTYL-3-(3-METHYLBENZYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-AMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:273 , ALA A:293 , LYS A:295 , ILE A:336 , GLU A:339 , MET A:341 , LEU A:393BINDING SITE FOR RESIDUE VGG A 601
2AC2SOFTWARELEU B:273 , ALA B:293 , LYS B:295 , ILE B:336 , GLY B:338 , GLU B:339 , MET B:341 , LEU B:393BINDING SITE FOR RESIDUE VGG B 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:334 -Tyr A:335

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LGG)

(-) 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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains d4lgga_ A: c-src tyrosine kinase                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...eeeeeee....eeeeee.....hhhhhhhhh.......eeee.....eeeee.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee........hhhhhhhh..hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lgg A 264 RESLRLEVKLGQGGEVWMGTWNGTTRVAIKTLKPGLQEAQVMKKLRHEKLVQLYAVVSEEIYIVGEYMSKGSLLDFLKGEMGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKDPEERPTFEYLQAFLEDYFTSTEPQYQPGENL 533
                                   273  ||   285       295    || 312       322       332|      343       353       363       373       383       393       403 ||    432       442       452       462       472       482       492       502       512       522       532 
                                      276|                  300|                     332|                                                                    405|                                                                                                            
                                       279                   308                      334                                                                     425                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains d4lggb_ B: c-src tyrosine kinase                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...eeeeeee...eeeeeee......hhhhhhhhhhhhh.........eeee.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lgg B 264 RESLRLEVKLGGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEYIVGEYMSKGSLLDFLKGEMGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKDPEERPTFEYLQAFLEDYFTSTEPQYQPGENL 533
                                   273||     287       297       307       317       327    || 339       349       359       369       379       389       399     ||428       438       448       458       468       478       488       498       508       518       528     
                                    274|                                                  332|                                                                   405|                                                                                                            
                                     279                                                   335                                                                    425
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (99, 99)

Asymmetric Unit(hide GO term definitions)

 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
    VGG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ile A:334 - Tyr A:335   [ 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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4lgg
    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
  SRC_CHICK | P00523
    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)
  2.7.10.2
    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
  SRC_CHICK | P00523
    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
        SRC_CHICK | P00523: 1f1w 1f2f 1nlo 1nlp 1p13 1prl 1prm 1rlp 1rlq 1srl 1srm 2hwo 2hwp 2oiq 2ptk 2qi8 2qlq 2qq7 3d7t 3d7u 3dqw 3dqx 3el7 3el8 3en4 3en5 3en6 3en7 3f3t 3f3u 3f3v 3f3w 3f6x 3fj5 3g5d 3g6g 3g6h 3geq 3lok 3oez 3of0 3qlf 3qlg 3svv 3tz7 3tz8 3tz9 3u4w 3u51 3uqf 3uqg 4agw 4dgg 4fic 4hvu 4hvv 4hvw 4jz3 4jz4 4le9 4lgh 4mcv 4o2p 4oml 4omm 4omn 4omo 4omp 4omq 4qt7 4rtu 4rtv 4rtw 4rtx 4rty 4rtz 4u5j 4ybj 4ybk 5bmm 5d10 5d11 5d12 5ec7 5eca 5i11 5j5s 5k9i 5oav 5ob0 5ob1 5ob2

(-) Related Entries Specified in the PDB File

4lgh CRYSTAL STRUCTURE OF 1NM-PP1 BOUND TO ANALOG-SENSITIVE SRC KINASE