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(-) Description

Title :  STRUCTURE OF ALG-2/HEBP2 COMPLEX
 
Authors :  X. Liu, J. Ma, H. Zhang, Y. Feng
Date :  08 Aug 16  (Deposition) - 02 Nov 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ef Hands, Complex, Calcium Ions, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ma, X. Zhang, Y. Feng, H. Zhang, X. Wang, Y. Zheng, W. Qiao, X. Liu
Structural And Functional Study Of Apoptosis-Linked Gene-2/Heme-Binding Protein 2 Interactions In Hiv-1 Production
J. Biol. Chem. 2016
PubMed: search  |  Reference-DOI: 10.1074/JBC.M116.752444

(-) Compounds

Molecule 1 - HEME-BINDING PROTEIN 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Strain: BL21-GOLD(DE3)PLYSS AG
    Expression System Taxid: 866768
    Fragment: UNP RESIDUES 20-197
    Gene: HEBP2, C6ORF34, SOUL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PLACENTAL PROTEIN 23,PP23,PROTEIN SOUL
 
Molecule 2 - PROGRAMMED CELL DEATH PROTEIN 6
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Strain: BL21-GOLD(DE3)PLYSS AG
    Expression System Taxid: 866768
    Fragment: UNP RESIDUES 24-191
    Gene: PDCD6, ALG2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: APOPTOSIS-LINKED GENE 2 PROTEIN,PROBABLE CALCIUM-BINDING PROTEIN ALG-2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP C:36 , ASP C:38 , SER C:40 , VAL C:42 , GLU C:47 , CL C:204binding site for residue CA C 201
2AC2SOFTWAREASP C:103 , ASP C:105 , SER C:107 , MET C:109 , GLU C:114binding site for residue CA C 202
3AC3SOFTWAREASP C:169 , ASP C:171 , ASP C:173 , TRP C:175 , HOH C:360binding site for residue CA C 203
4AC4SOFTWAREGLN B:149 , GLU B:153 , ASP C:38 , SER C:40 , VAL C:42 , GLU C:47 , CA C:201 , HOH C:344binding site for residue CL C 204
5AC5SOFTWAREASP D:36 , ASP D:38 , SER D:40 , VAL D:42 , GLU D:47 , CL D:204binding site for residue CA D 201
6AC6SOFTWAREASP D:103 , ASP D:105 , SER D:107 , MET D:109 , GLU D:114binding site for residue CA D 202
7AC7SOFTWAREASP D:169 , ASP D:171 , ASP D:173 , TRP D:175binding site for residue CA D 203
8AC8SOFTWAREGLU A:153 , ASP D:38 , SER D:40 , VAL D:42 , GLU D:47 , CA D:201 , HOH D:313binding site for residue CL D 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Ala A:31 -Gly A:32
2Ala A:87 -Pro A:88
3Gly A:96 -Ser A:97
4Ser A:97 -Gly A:98
5Ser A:181 -Pro A:182
6Gly B:32 -Pro B:33
7Ala B:87 -Pro B:88
8Ser B:181 -Pro B:182
9Phe C:188 -Ser C:189
10Asp D:171 -Gln D:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GQQ)

(-) 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:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee............eeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhh.............eeeeee........eeeeeeee.hhhhhh.........eeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhh........eeeee...........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gqq A  20 VETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQK 197
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189        


Chain B from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee............eeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhh..............eeeeee........eeeeeeee.hhhhhh.........eeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhh........eeeee...........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gqq B  20 VETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQK 197
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189        


Chain C from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh......eehhhhhhhh........hhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gqq C  22 GSDQSFLWNVFQRVDKDRSGVISDTELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFSIV 191
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191


Chain D from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh......eehhhhhhhh........hhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gqq D  22 GSDQSFLWNVFQRVDKDRSGVISDTELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVF 188
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
   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 5GQQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (40, 43)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:31 - Gly A:32   [ RasMol ]  
    Ala A:87 - Pro A:88   [ RasMol ]  
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    Asp D:171 - Gln D:172   [ RasMol ]  
    Gly A:96 - Ser A:97   [ RasMol ]  
    Gly B:32 - Pro B:33   [ RasMol ]  
    Phe C:188 - Ser C:189   [ RasMol ]  
    Ser A:181 - Pro A:182   [ RasMol ]  
    Ser A:97 - Gly A:98   [ RasMol ]  
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  5gqq
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  HEBP2_HUMAN | Q9Y5Z4
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  PDCD6_HUMAN | O75340
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 Related Entries

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

UniProtKB/Swiss-Prot
        HEBP2_HUMAN | Q9Y5Z4: 3r85 3r8j 3r8k 4ayz 4b0y
        PDCD6_HUMAN | O75340: 2zn8 2zn9 2znd 2zne 2zrs 2zrt 3aaj 3aak 3wxa

(-) Related Entries Specified in the PDB File

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