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(-) Description

Title :  STRUCTURE OF THE CARD-CARD DISK
 
Authors :  S. C. Lin, Y. C. Lo, T. W. Su
Date :  24 Dec 16  (Deposition) - 19 Apr 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Protein-Protein Interaction, Signaling Protein Complex, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. W. Su, C. Y. Yang, W. P. Kao, B. J. Kuo, S. M. Lin, J. Y. Lin, Y. C. Lo, S. C. Lin
Structural Insights Into Dd-Fold Assembly And Caspase-9 Activation By The Apaf-1 Apoptosome.
Structure V. 25 407 2017
PubMed-ID: 28111022  |  Reference-DOI: 10.1016/J.STR.2016.12.019

(-) Compounds

Molecule 1 - APOPTOTIC PROTEASE-ACTIVATING FACTOR 1
    Chains: C, A, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-95
    Gene: APAF1, KIAA0413
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: APAF-1
 
Molecule 2 - CASPASE
    Chains: D, B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-128
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1CSO3Mod. Amino AcidS-HYDROXYCYSTEINE
2IOD11Ligand/IonIODIDE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR C:22binding site for residue IOD C 101
2AC2SOFTWAREARG D:290 , ARG D:293binding site for residue IOD D 401
3AC3SOFTWAREARG D:211binding site for residue IOD D 403
4AC4SOFTWAREARG B:290 , ARG B:293binding site for residue IOD B 401
5AC5SOFTWARETHR E:22binding site for residue IOD E 101
6AC6SOFTWARESER D:231 , ARG F:293binding site for residue IOD F 1201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys D:300 -Pro D:301
2Lys B:300 -Pro B:301

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5WVC)

(-) 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:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5wvc A   1 MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVS  95
                                    10        20        30        40        50        60        70        80        90     


Chain B from PDB  Type:PROTEIN  Length:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 5wvc B 199 ASMDEADRRLLRRcRLRLVEELQVDQLWDVLLSRELFRPHMIEDIQRAGSGSRRDQARQLIIDLETRGSQALPLFISCLEDTGQDMLASFLRTNRQAAKLSKP 301
                                   208   |   218       228       238       248       258       268       278       288       298   
                                       212-CSO                                                                                     


Chain C from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5wvc C   1 MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVS  95
                                    10        20        30        40        50        60        70        80        90     


Chain D from PDB  Type:PROTEIN  Length:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 5wvc D 199 ASMDEADRRLLRRcRLRLVEELQVDQLWDVLLSRELFRPHMIEDIQRAGSGSRRDQARQLIIDLETRGSQALPLFISCLEDTGQDMLASFLRTNRQAAKLSKP 301
                                   208   |   218       228       238       248       258       268       278       288       298   
                                       212-CSO                                                                                     


Chain E from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 5wvc E   1 MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVV  94
                                    10        20        30        40        50        60        70        80        90    


Chain F from PDB  Type:PROTEIN  Length:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 5wvc F 199 ASMDEADRRLLRRcRLRLVEELQVDQLWDVLLSRELFRPHMIEDIQRAGSGSRRDQARQLIIDLETRGSQALPLFISCLEDTGQDMLASFLRTNRQAAKLSKP 301
                                   208   |   218       228       238       248       258       268       278       288       298   
                                       212-CSO
   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 5WVC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 44)

Asymmetric/Biological Unit(hide GO term definitions)

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  5wvc
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 Related Entries

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

UniProtKB/Swiss-Prot
        A8K7U6_HUMAN | A8K7U6: 5wve
        APAF_HUMAN | O14727: 1c15 1cww 1cy5 1z6t 2p1h 2ygs 3j2t 3jbt 3ygs 4rhw 5juy 5wve

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5WVC)