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
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)

(-) Description

Title :  BCL-XL WITH BAK BH3 COMPLEX
 
Authors :  W. D. Fairlie, E. F. Lee, B. J. Smith, P. E. Czabotar, P. M. Colman
Date :  06 Nov 15  (Deposition) - 01 Jun 16  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Bcl-Xl, Bak, Bh3 Domain, Apoptosis, Bcl-2 Family (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. F. Lee, S. Grabow, S. Chappaz, G. Dewson, C. Hockings, R. M. Kluck, D. H. Gray, M. T. Witkowski, M. Evangelista, A. Pettikiriarachchi, P. Bouillet, R. M. Lane, P. E. Czabotar, P. M. Colman, B. J. Smith, B. T. Kile, W. D. Fairlie
Physiological Restraint Of Bak By Bcl-Xl Is Essential For Cell Survival.
Genes Dev. V. 30 1240 2016
PubMed-ID: 27198225  |  Reference-DOI: 10.1101/GAD.279414.116

(-) Compounds

Molecule 1 - BCL-XL
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI,
    Expression System Plasmid: PGEX6P3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-26,83-209
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BCL2-L-1, APOPTOSIS REGULATOR BCL-X
 
Molecule 2 - BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
    Chains: B
    Fragment: BH3 DOMAIN, UNP RESIDUES 63-96
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: APOPTOSIS REGULATOR BAK, BCL-2-LIKE PROTEIN 7, BCL2-L-7, BAK
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:133 , ASN A:136 , TRP A:137 , TRP A:181 , LEU A:194 , ASN B:86 , ARG B:87 , ARG B:88BINDING SITE FOR RESIDUE GOL A1208
2AC2SOFTWAREGLY A:117 , ARG A:165 , HOH A:2085 , ILE B:80 , HOH B:2008BINDING SITE FOR RESIDUE GOL A1209
3AC3SOFTWAREASP A:67 , SER A:70 , ALA A:84 , GLN A:88 , ARG A:91BINDING SITE FOR RESIDUE GOL A1210
4AC4SOFTWAREASP A:133 , ASN A:136 , ARG A:139 , HOH A:2078 , ASP B:83 , ARG B:88 , HOH B:2005BINDING SITE FOR RESIDUE GOL B1106

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FMK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FMK)

(-) 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:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fmk A  58 SQSNRELVVDFLSYKLSQKGYSWSQMAAVKQALREAGDEFELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIASWMATYLNDHLEPWIQENGGWDTFVELYGNNAAAESRKGQ 207
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207


Chain B from PDB  Type:PROTEIN  Length:21
                                                     
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 5fmk B  69 STMGQVGRQLAIIGDDINRRY  89
                                    78        88
   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 5FMK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (129, 149)

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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5fmk)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  5fmk
    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
  B2CL1_HUMAN | Q07817
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  BAK_HUMAN | Q16611
    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)
  (no 'Enzyme Classificator' available)
    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
  B2CL1_HUMAN | Q07817
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  BAK_HUMAN | Q16611
    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
        B2CL1_HUMAN | Q07817: 1bxl 1g5j 1g5m 1gjh 1lxl 1maz 1r2d 1r2e 1r2g 1r2h 1r2i 1ysg 1ysi 1ysn 2b48 2lp8 2lpc 2m03 2m04 2me8 2me9 2mej 2o1y 2o21 2o22 2o2m 2o2n 2p1l 2pon 2yj1 2yq6 2yq7 2yxj 3cva 3fdl 3fdm 3inq 3io8 3pl7 3qkd 3r85 3sp7 3spf 3wiz 3zk6 3zln 3zlo 3zlr 4a1u 4a1w 4aq3 4bpk 4c52 4c5d 4cin 4ehr 4hnj 4ieh 4ppi 4qve 4qvf 4qvx 4tuh 4z9v 5agw 5agx 5b1z 5c3g 5fmj
        BAK_HUMAN | Q16611: 1bxl 2ims 2imt 2jby 2jcn 2lp8 2m5b 2xpx 2yv6 3i1h 3qbr 4d2l 4u2u 4u2v 4uf1 5ajk 5fmi

(-) Related Entries Specified in the PDB File

5fmi HUMAN BAK Q77L
5fmj BCL-XL WITH MOUSE BAK BH3 Q75L COMPLEX