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 :  CIAP1-BIR3 IN COMPLEX WITH A DIVALENT SMAC MIMETIC
 
Authors :  F. Cossu, E. Mastrangelo, M. Bolognesi, M. Milani
Date :  23 Mar 12  (Deposition) - 05 Dec 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Zinc Finger, Apoptosis Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Cossu, M. Milani, P. Vachette, F. Malvezzi, S. Grassi, D. Lecis, D. Delia, C. Drago, P. Seneci, M. Bolognesi, E. Mastrangelo
Structural Insight Into Inhibitor Of Apoptosis Proteins Recognition By A Potent Divalent Smac-Mimetic.
Plos One V. 7 49527 2012
PubMed-ID: 23166698  |  Reference-DOI: 10.1371/JOURNAL.PONE.0049527

(-) Compounds

Molecule 1 - BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 2
    Chains: A, B, C, D
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: BIR3 DOMAIN (UNP RESIDUES 251-363)
    Gene: BIRC2, API1, IAP2, MIHB, RNF48
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: C-IAP1, IAP HOMOLOG B, INHIBITOR OF APOPTOSIS PROTEIN 2, IAP-2, HIAP-2, HIAP2, RING FINGER PROTEIN 48, TNFR2-TRAF-SIGNALING COMPLEX PROTEIN 2

 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
10O62Ligand/Ion(3S,6S,7S,9AS,3'S,6'S,7'S,9A'S)-N,N'-(BENZENE-1,4-DIYLBIS{BUTANE-4,1-DIYL-1H-1,2,3-TRIAZOLE-1,4-DIYL[(S)-PHENYLMETHANEDIYL]})BIS[7-(HYDROXYMETHYL)-6-{[(2S)-2-(METHYLAMINO)BUTANOYL]AMINO}-5-OXOOCTAHYDRO-1H-PYRROLO[1,2-A]AZEPINE-3-CARBOXAMIDE]
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
10O61Ligand/Ion(3S,6S,7S,9AS,3'S,6'S,7'S,9A'S)-N,N'-(BENZENE-1,4-DIYLBIS{BUTANE-4,1-DIYL-1H-1,2,3-TRIAZOLE-1,4-DIYL[(S)-PHENYLMETHANEDIYL]})BIS[7-(HYDROXYMETHYL)-6-{[(2S)-2-(METHYLAMINO)BUTANOYL]AMINO}-5-OXOOCTAHYDRO-1H-PYRROLO[1,2-A]AZEPINE-3-CARBOXAMIDE]
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10O61Ligand/Ion(3S,6S,7S,9AS,3'S,6'S,7'S,9A'S)-N,N'-(BENZENE-1,4-DIYLBIS{BUTANE-4,1-DIYL-1H-1,2,3-TRIAZOLE-1,4-DIYL[(S)-PHENYLMETHANEDIYL]})BIS[7-(HYDROXYMETHYL)-6-{[(2S)-2-(METHYLAMINO)BUTANOYL]AMINO}-5-OXOOCTAHYDRO-1H-PYRROLO[1,2-A]AZEPINE-3-CARBOXAMIDE]
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:300 , CYS A:303 , HIS A:320 , CYS A:327BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWARECYS B:300 , CYS B:303 , HIS B:320 , CYS B:327BINDING SITE FOR RESIDUE ZN B 401
3AC3SOFTWARECYS C:300 , CYS C:303 , HIS C:320 , CYS C:327BINDING SITE FOR RESIDUE ZN C 401
4AC4SOFTWAREASP A:297 , VAL A:298 , LYS A:299 , GLY A:306 , LEU A:307 , ARG A:308 , CYS A:309 , ASP A:314 , GLU A:319 , TRP A:323 , LEU A:353 , ASP C:297 , GLY C:306 , LEU C:307 , ARG C:308 , CYS C:309 , GLU C:311 , ASP C:314 , GLU C:319 , TRP C:323 , THR C:356BINDING SITE FOR RESIDUE 0O6 C 402
5AC5SOFTWARECYS D:300 , CYS D:303 , HIS D:320 , CYS D:327BINDING SITE FOR RESIDUE ZN D 401
6AC6SOFTWAREASP B:297 , GLY B:306 , LEU B:307 , ARG B:308 , CYS B:309 , ASP B:314 , GLU B:319 , TRP B:323 , LEU B:353 , ASP D:297 , GLY D:306 , LEU D:307 , ARG D:308 , CYS D:309 , ASP D:314 , GLU D:319 , TRP D:323 , LEU D:353 , HOH D:525 , HOH D:529BINDING SITE FOR RESIDUE 0O6 D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EB9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EB9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EB9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EB9)

(-) Exons   (0, 0)

(no "Exon" information available for 4EB9)

(-) 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:102
                                                                                                                                      
               SCOP domains d4eb9a_ A: 2MIHB/C-IAP-1                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh......hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4eb9 A 254 SISNLSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFCCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQGRYPHLLEQLLS 355
                                   263       273       283       293       303       313       323       333       343       353  


Chain B from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains d4eb9b_ B: 2MIHB/C-IAP-1                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh......hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4eb9 B 254 SISNLSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFCCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQGRYPHLLEQLL 354
                                   263       273       283       293       303       313       323       333       343       353 


Chain C from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains d4eb9c_ C: 2MIHB/C-IAP-1                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..........hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4eb9 C 255 ISNLSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFCCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQGRYPHLLEQLLST 356
                                   264       274       284       294       304       314       324       334       344       354  


Chain D from PDB  Type:PROTEIN  Length:103
                                                                                                                                       
               SCOP domains d4eb9d_ D: 2MIHB/C-IAP-1                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhh..........hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 4eb9 D 254 SISNLSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFCCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQGRYPHLLEQLLST 356
                                   263       273       283       293       303       313       323       333       343       353
   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, 4)

Asymmetric Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EB9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EB9)

(-) Gene Ontology  (60, 60)

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
    0O6  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4eb9)
 
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
  4eb9
    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
  BIRC2_HUMAN | Q13490
    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)
  6.3.2.-
    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
  BIRC2_HUMAN | Q13490
    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
        BIRC2_HUMAN | Q13490: 1qbh 2l9m 3d9t 3d9u 3m1d 3mup 3oz1 3t6p 3uw4 4hy4 4hy5 4kmn 4lge 4lgu 4mti 4mu7 5m6n

(-) Related Entries Specified in the PDB File

3mup CIAP1-BIR3 DOMAIN IN COMPLEX WITH THE SMAC-MIMETIC COMPOUND SMAC037
3oz1 CIAP1-BIR3 DOMAIN IN COMPLEX WITH THE SMAC-MIMETIC COMPOUND SMAC066
4ec4