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(-) Description

Title :  CRYSTAL STRUCTURE OF XIAP BIR3 WITH CS3
 
Authors :  S. G. Hymowitz
Date :  26 May 09  (Deposition) - 16 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Bir, Iap, Apoptosis, Small Molecule Drug Discovery, Structure-Based Drug Design, Ligase, Metal-Binding, Phosphoprotein, Protease Inhibitor, Thiol Protease Inhibitor, Ubl Conjugation Pathway, Zinc- Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Ndubaku, E. Varfolomeev, L. Wang, K. Zobel, K. Lau, L. O. Elliott, B. Maurer, A. V. Fedorova, J. N. Dynek, M. Koehler, S. G. Hymowitz, V. Tsui, K. Deshayes, W. J. Fairbrother, J. A. Flygare, D. Vucic
Antagonism Of C-Iap And Xiap Proteins Is Required For Efficient Induction Of Cell Death By Small-Molecule Iap Antagonists.
Acs Chem. Biol. V. 4 557 2009
PubMed-ID: 19492850  |  Reference-DOI: 10.1021/CB900083M

(-) Compounds

Molecule 1 - BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4
    ChainsA, B
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL-21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentBIR3, UNP RESIDUES 256-346
    GeneAPI3, BIRC4, IAP3, XIAP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymE3 UBIQUITIN-PROTEIN LIGASE XIAP, INHIBITOR OF APOPTOSIS PROTEIN 3, X-LINKED INHIBITOR OF APOPTOSIS PROTEIN, X-LINKED IAP, IAP-LIKE PROTEIN, HILP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
19JZ2Ligand/Ion(3S)-1-{(2S)-2-CYCLOHEXYL-2-[(N-METHYL-L-ALANYL)AMINO]ACETYL}-3-METHYL-N-(2-PYRIMIDIN-2-YLPHENYL)-L-PROLINAMIDE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
19JZ1Ligand/Ion(3S)-1-{(2S)-2-CYCLOHEXYL-2-[(N-METHYL-L-ALANYL)AMINO]ACETYL}-3-METHYL-N-(2-PYRIMIDIN-2-YLPHENYL)-L-PROLINAMIDE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
19JZ1Ligand/Ion(3S)-1-{(2S)-2-CYCLOHEXYL-2-[(N-METHYL-L-ALANYL)AMINO]ACETYL}-3-METHYL-N-(2-PYRIMIDIN-2-YLPHENYL)-L-PROLINAMIDE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:300 , CYS A:303 , HIS A:320 , CYS A:327BINDING SITE FOR RESIDUE ZN A 502
2AC2SOFTWARECYS B:300 , CYS B:303 , HIS B:320 , CYS B:327BINDING SITE FOR RESIDUE ZN B 502
3AC3SOFTWARE9JZ A:1 , HOH A:141 , LYS A:322 , TRP A:323 , PRO A:325 , HIS A:346 , HOH B:55 , GLY B:306 , LEU B:307 , THR B:308 , ASP B:309 , TRP B:310 , GLU B:314 , GLN B:319 , TRP B:323 , TYR B:324BINDING SITE FOR RESIDUE 9JZ B 1
4AC4SOFTWAREHOH A:159 , GLY A:306 , LEU A:307 , THR A:308 , ASP A:309 , GLU A:314 , GLN A:319 , LYS A:322 , TRP A:323 , TYR A:324 , 9JZ B:1 , ASP B:309BINDING SITE FOR RESIDUE 9JZ A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HL5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu B:256 -Pro B:257

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HL5)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIR_REPEAT_1PS01282 BIR repeat.XIAP_HUMAN26-93
163-230
265-330
 
  2-
-
A:265-330
B:265-330
2BIR_REPEAT_2PS50143 BIR repeat profile.XIAP_HUMAN29-94
166-231
268-331
 
  2-
-
A:268-331
B:268-331
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIR_REPEAT_1PS01282 BIR repeat.XIAP_HUMAN26-93
163-230
265-330
 
  1-
-
A:265-330
-
2BIR_REPEAT_2PS50143 BIR repeat profile.XIAP_HUMAN29-94
166-231
268-331
 
  1-
-
A:268-331
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIR_REPEAT_1PS01282 BIR repeat.XIAP_HUMAN26-93
163-230
265-330
 
  1-
-
-
B:265-330
2BIR_REPEAT_2PS50143 BIR repeat profile.XIAP_HUMAN29-94
166-231
268-331
 
  1-
-
-
B:268-331

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003711992aENSE00001810722X:122993877-122994143267XIAP_HUMAN-00--
1.3cENST000003711993cENSE00002176074X:123019481-123020389909XIAP_HUMAN1-2932932A:253-293
B:256-293
41
38
1.4bENST000003711994bENSE00001649641X:123022469-123022568100XIAP_HUMAN293-326342A:293-326
B:293-326
34
34
1.5bENST000003711995bENSE00001630752X:123025088-12302516679XIAP_HUMAN326-352272A:326-346
B:326-345
21
20
1.6ENST000003711996ENSE00001714518X:123026581-12302662343XIAP_HUMAN353-367150--
1.7bENST000003711997bENSE00001653318X:123034343-123034543201XIAP_HUMAN367-434680--
1.8eENST000003711998eENSE00001454620X:123040838-1230478296992XIAP_HUMAN434-497640--

(-) 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:94
 aligned with XIAP_HUMAN | P98170 from UniProtKB/Swiss-Prot  Length:497

    Alignment length:94
                                   262       272       282       292       302       312       322       332       342    
           XIAP_HUMAN   253 STNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTH 346
               SCOP domains d3hl5a_ A: automated matches                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh........hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------BIR_REPEAT_1  PDB: A:265-330 UniProt: 265-330                     ---------------- PROSITE (1)
                PROSITE (2) ---------------BIR_REPEAT_2  PDB: A:268-331 UniProt: 268-331                   --------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3c  PDB: A:253-293 UniProt: 1-293 --------------------------------Exon 1.5b             Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.4b  PDB: A:293-326         -------------------- Transcript 1 (2)
                 3hl5 A 253 SHMLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTH 346
                                   262       272       282       292       302       312       322       332       342    

Chain B from PDB  Type:PROTEIN  Length:90
 aligned with XIAP_HUMAN | P98170 from UniProtKB/Swiss-Prot  Length:497

    Alignment length:90
                                   265       275       285       295       305       315       325       335       345
           XIAP_HUMAN   256 LPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLT 345
               SCOP domains d3hl5b_ B: automated matches                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh......hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------BIR_REPEAT_1  PDB: B:265-330 UniProt: 265-330                     --------------- PROSITE (1)
                PROSITE (2) ------------BIR_REPEAT_2  PDB: B:268-331 UniProt: 268-331                   -------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3c  PDB: B:256-293 [INCOMPLETE]--------------------------------Exon 1.5b            Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.4b  PDB: B:293-326         ------------------- Transcript 1 (2)
                 3hl5 B 256 LPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLT 345
                                   265       275       285       295       305       315       325       335       345

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HL5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HL5)

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (XIAP_HUMAN | P98170)
molecular function
    GO:0004869    cysteine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0043027    cysteine-type endopeptidase inhibitor activity involved in apoptotic process    Stops, prevents or reduces the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0055070    copper ion homeostasis    Any process involved in the maintenance of an internal steady state of copper ions within an organism or cell.
    GO:1990001    inhibition of cysteine-type endopeptidase activity involved in apoptotic process    Any process that prevents the activation of an inactive cysteine-type endopeptidase involved in an apoptotic process.
    GO:0090307    mitotic spindle assembly    The aggregation, arrangement and bonding together of a set of components to form the spindle that contributes to the process of mitosis.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0090263    positive regulation of canonical Wnt signaling pathway    Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:1902530    positive regulation of protein linear polyubiquitination    Any process that activates or increases the frequency, rate or extent of protein linear polyubiquitination.
    GO:0031398    positive regulation of protein ubiquitination    Any process that activates or increases the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0030510    regulation of BMP signaling pathway    Any process that modulates the frequency, rate or extent of the activity of any BMP receptor signaling pathway.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0045088    regulation of innate immune response    Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    GO:0070424    regulation of nucleotide-binding oligomerization domain containing signaling pathway    Any process that modulates the frequency, rate, or extent of a nucleotide-binding oligomerization domain containing (NOD) pathway.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005876    spindle microtubule    Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.

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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 3uw4 3uw5 4ec4 4hy0 4ic2 4ic3 4j3y 4j44 4j45 4j46 4j47 4j48 4kju 4kjv 4kmp 4mtz 4oxc 4wvs 4wvt 4wvu 5c0k 5c0l 5c3h 5c3k 5c7a 5c7b 5c7c 5c7d 5c83 5c84 5m6e 5m6f 5m6h 5m6l 5m6m

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3HL5)