Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  SRC IN COMPLEX WITH DNA-TEMPLATED MACROCYCLIC INHIBITOR MC25B
 
Authors :  G. Georghiou, K. E. Guja, S. Aleem, R. E. Kleiner, D. R. Liu, W. T. Miller, Diaz, M. A. Seeliger
Date :  22 May 15  (Deposition) - 21 Sep 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. U. Aleem, G. Georghiou, R. E. Kleiner, K. E. Guja, B. P. Craddock, A. Lyczek, A. I. Chan, M. Garcia-Diaz, W. T. Miller, D. R. Liu, M. A. Seeliger
Structural And Biochemical Basis For Intracellular Kinase Inhibition By Src-Specific Peptidic Macrocycles.
Cell Chem Biol V. 23 1103 2016
PubMed-ID: 27593110  |  Reference-DOI: 10.1016/J.CHEMBIOL.2016.07.017

(-) Compounds

Molecule 1 - PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC
    Chains: A, B
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: SRC
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Synonym: PROTO-ONCOGENE C-SRC,PP60C-SRC,P60-SRC
 
Molecule 2 - MACROCYCLIC INHIBITOR MC25B
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
1ALC2OTHER2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
2FUM2OTHERFUMARIC ACID
3ORN2OTHERL-ORNITHINE
4PFF2OTHER4-FLUORO-L-PHENYLALANINE
5PPN2OTHERPARA-NITROPHENYLALANINE
Biological Unit 1 (5, 5)
No.NameCountTypeFull Name
1ALC1OTHER2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
2FUM1OTHERFUMARIC ACID
3ORN1OTHERL-ORNITHINE
4PFF1OTHER4-FLUORO-L-PHENYLALANINE
5PPN1OTHERPARA-NITROPHENYLALANINE
Biological Unit 2 (5, 5)
No.NameCountTypeFull Name
1ALC1OTHER2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
2FUM1OTHERFUMARIC ACID
3ORN1OTHERL-ORNITHINE
4PFF1OTHER4-FLUORO-L-PHENYLALANINE
5PPN1OTHERPARA-NITROPHENYLALANINE

(-) Sites  (0, 0)

(no "Site" information available for 5BMM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BMM)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:332 -Pro A:333
2Glu B:332 -Pro B:333

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BMM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BMM)

(-) Exons   (0, 0)

(no "Exon" information available for 5BMM)

(-) 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:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhheeeeeeee...eeeeeee.....eeeeeee.....hhhhhhhhhhhhhhh.......eeeee.....eeeee....eehhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee...hhhhhh.hhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bmm A 259 AWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGEMGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKDPEERPTFEYLQAFLEDYFTSTEPQYQPGENL 533
                                   268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528     


Chain B from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeeee...eeeeeeee...eeeeeeee.....hhhhhhhhhhhhhhh.......eeeee.....eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee..........hhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bmm B 259 AWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGEMGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKDPEERPTFEYLQAFLEDYFTSTEPQYQPGENL 533
                                   268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528     


Chain C from PDB  Type:OTHER  Length:5
                                     
                 5bmm C   1 xxxxx   5
                            |||||
                            1-FUM
                             2-ALC
                              3-PFF
                               4-PPN
                                5-ORN


Chain D from PDB  Type:OTHER  Length:5
                                     
                 5bmm D   1 xxxxx   5
                            |||||
                            |||||
                            1-FUM
                             2-ALC
                              3-PFF
                               4-PPN
                                5-ORN
   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 5BMM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BMM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BMM)

(-) 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
    ALC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FUM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ORN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PFF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PPN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 5bmm)
 
  Cis Peptide Bonds
    Glu A:332 - Pro A:333   [ RasMol ]  
    Glu B:332 - Pro B:333   [ 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 | Biol. Unit 1 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
  5bmm
    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 4lgg 4lgh 4mcv 4o2p 4oml 4omm 4omn 4omo 4omp 4omq 4qt7 4rtu 4rtv 4rtw 4rtx 4rty 4rtz 4u5j 4ybj 4ybk 5d10 5d11 5d12 5ec7 5eca 5i11 5j5s 5k9i 5oav 5ob0 5ob1 5ob2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5BMM)