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(-) Description

Title :  CRYSTAL STRUCTURE OF XIAP-BIR2 DOMAIN COMPLEXED WITH (S)-3-(4-METHOXYPHENYL)-2-((S)-2-((S)-1-((S)-2-((S)-2-(METHYLAMINO) PROPANAMIDO)PENT-4-YNOYL)PYRROLIDINE-2-CARBOXAMIDO)-3-PHENYLPROPANAMIDO)PROPANOIC ACID
 
Authors :  M. E. Pokross
Date :  07 Nov 14  (Deposition) - 06 May 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A,B
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
    Chains: A
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 156-231
    Gene: XIAP, API3, BIRC4, IAP3
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BACULOVIRAL 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
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
14LZ1Mod. Amino AcidO-[2-(TRIAZA-1,2-DIEN-2-IUM-1-YL)ETHYL]-L-TYROSINE
2GOL1Ligand/IonGLYCEROL
3LPH1Mod. Amino AcidL-PROPARGYLGLYCINE
4MAA1Mod. Amino AcidN-METHYL-L-ALANINE
5SO43Ligand/IonSULFATE ION
6ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:200 , CYS A:203 , HIS A:220 , CYS A:227binding site for residue ZN A 501
2AC2SOFTWAREHIS A:-2 , GLY A:-3 , GLU A:164 , ALA A:202 , CYS A:203 , ASN A:226 , PHE A:228binding site for residue SO4 A 502
3AC3SOFTWAREGLN A:197 , LYS A:208 , ASN A:209 , HOH A:606 , HOH A:607 , HOH A:609binding site for residue SO4 A 503
4AC4SOFTWARELYS A:206 , PHE B:4 , 4LZ B:5binding site for residue GOL A 504
5AC5SOFTWARECYS A:203 , GLY A:205 , PHE A:224 , ASN A:226binding site for residue SO4 A 505

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WVS)

(-) Sequences/Alignments

Asymmetric/Biological 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 ....hhhhhhhhhhhhh....hhhhh.hhhhhhhh.eee......eee.....eee......hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 4wvs A  -3 GHMRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGDQVQCFACGGKLKNWEPGDRAWSEHRRHFPNCFFVL 231
                              ||   162       172       182       192       202       212       222         
                             -1|                                                                           
                             156                                                                           


Chain B from PDB  Type:PROTEIN  Length:5
                                     
               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
                 4wvs B   1 xxPFx   5
                            ||  |
                            1-MAA
                             2-LPH
                                5-4LZ
   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 4WVS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric/Biological 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 | P98170: 1c9q 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 4wvt 4wvu 5c0k 5c0l 5c3h 5c3k 5c7a 5c7b 5c7c 5c7d 5c83 5c84 5m6e 5m6f 5m6h 5m6l 5m6m

(-) Related Entries Specified in the PDB File

4wvt 4wvu