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(-) Description

Title :  CRYSTAL STRUCTURE OF XIAP-BIR2 DOMAIN COMPLEXED WITH LIGAND BOUND
 
Authors :  M. E. Pokross
Date :  07 Nov 14  (Deposition) - 04 Mar 15  (Release) - 08 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Iap, Xiap-Bir2, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. A. Seigal, W. H. Connors, A. Fraley, R. M. Borzilleri, P. H. Carter, S. L. Emanuel, J. Fargnoli, K. Kim, M. Lei, J. G. Naglich, M. E. Pokross, S. L. Posy, H. Shen, N. Surti, R. Talbott, Y. Zhang, N. K. Terrett
The Discovery Of Macrocyclic Xiap Antagonists From A Dna-Programmed Chemistry Library, And Their Optimization To Give Lead Compounds With In Vivo Antitumor Activity.
J. Med. Chem. V. 58 2855 2015
PubMed-ID: 25695766  |  Reference-DOI: 10.1021/JM501892G

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE XIAP
    ChainsA, B
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneXIAP, API3, BIRC4, IAP3
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4,IAP-LIKE PROTEIN,HILP,INHIBITOR OF APOPTOSIS PROTEIN 3,HIAP3,X-LINKED INHIBITOR OF APOPTOSIS PROTEIN,X-LINKED IAP
 
Molecule 2 - 3,11-DIFLUORO-6,8,13-TRIMETHYL-8H-QUINO[4,3,2-KL]ACRIDIN- 13-IUM
    ChainsC, D
    EngineeredYES
    SyntheticYES

 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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
13V72Mod. Amino Acid3-[4-(HYDROXYMETHYL)-1H-1,2,3-TRIAZOL-1-YL]PROPAN-1-OL
2MAA2Mod. Amino AcidN-METHYL-L-ALANINE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
13V71Mod. Amino Acid3-[4-(HYDROXYMETHYL)-1H-1,2,3-TRIAZOL-1-YL]PROPAN-1-OL
2MAA1Mod. Amino AcidN-METHYL-L-ALANINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
13V71Mod. Amino Acid3-[4-(HYDROXYMETHYL)-1H-1,2,3-TRIAZOL-1-YL]PROPAN-1-OL
2MAA1Mod. Amino AcidN-METHYL-L-ALANINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:200 , CYS A:203 , HIS A:220 , CYS A:227BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWARECYS B:200 , CYS B:203 , HIS B:220 , CYS B:227BINDING SITE FOR RESIDUE ZN B 301
3AC3SOFTWAREGLN A:197 , LYS A:206 , LEU A:207 , LYS A:208 , ASN A:209 , TRP A:210 , GLU A:211 , ASP A:214 , GLU A:219 , HIS A:223 , PHE A:224 , LEU B:167 , GLN B:171 , PRO B:181 , HOH C:101 , HOH C:102 , HOH C:103 , HOH C:108BINDING SITE FOR CHAIN C OF 3,11-DIFLUORO-6,8,13 -TRIMETHYL-8H-QUINO[4,3,2-KL]ACRIDIN- 13-IUM
4AC4SOFTWARELEU A:167 , GLN A:171 , PRO A:181 , GLN B:197 , LYS B:206 , LEU B:207 , LYS B:208 , ASN B:209 , TRP B:210 , GLU B:211 , ASP B:214 , GLU B:219 , HIS B:223 , PHE B:224 , HOH D:101 , HOH D:102 , HOH D:103 , HOH D:104 , HOH D:105BINDING SITE FOR CHAIN D OF 3,11-DIFLUORO-6,8,13 -TRIMETHYL-8H-QUINO[4,3,2-KL]ACRIDIN- 13-IUM

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:-3 -His A:-2
2Gly B:-3 -His B:-2

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WVT)

(-) 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:79
                                                                                                               
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh...hhhhh.hhhhhhhh.eee......eee.....eee......hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 4wvt A  -3 GHMRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGDQVQCFACGGKLKNWEPGDRAWSEHRRHFPNCFFVL 231
                              ||   162       172       182       192       202       212       222         
                             -1|                                                                           
                             156                                                                           

Chain B from PDB  Type:PROTEIN  Length:79
                                                                                                               
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh...hhhhh.hhhhhhhh.eee......eee.....eee......hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 4wvt B  -3 GHMRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGDQVQCFACGGKLKNWEPGDRAWSEHRRHFPNCFFVL 231
                              ||   162       172       182       192       202       212       222         
                             -1|                                                                           
                             156                                                                           

Chain C from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author .eee.. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4wvt C   1 xFPFFx   6
                            |    |
                            1-MAA|
                                 6-3V7

Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author .eee.. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4wvt D   1 xFPFFx   6
                            |    |
                            |    |
                            1-MAA|
                                 6-3V7

   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 4WVT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        XIAP_HUMAN | P981701c9q 1f9x 1g3f 1g73 1i3o 1i4o 1i51 1kmc 1nw9 1tfq 1tft 2ecg 2jk7 2kna 2opy 2opz 2poi 2pop 2qra 2vsl 3clx 3cm2 3cm7 3eyl 3g76 3hl5 3uw4 3uw5 4ec4 4hy0 4ic2 4ic3 4j3y 4j44 4j45 4j46 4j47 4j48 4kju 4kjv 4kmp 4mtz 4oxc 4wvs 4wvu 5c0k 5c0l 5c3h 5c3k 5c7a 5c7b 5c7c 5c7d 5c83 5c84 5m6e 5m6f 5m6h 5m6l 5m6m

(-) Related Entries Specified in the PDB File

4wvs 4wvu