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(-) Description

Title :  CRYSTAL STRUCTURE OF GEODIA CYDONIUM BHP2 IN COMPLEX WITH LUBOMIRSKIA BAICALENSIS BAK-2
 
Authors :  S. Caria, M. G. Hinds, M. Kvansakul
Date :  12 Nov 16  (Deposition) - 25 Jan 17  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Bhp2, Lb-Bak-2, Apoptosis, Sponge, Bcl-2 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Caria, M. G. Hinds, M. Kvansakul
Structural Insight Into An Evolutionarily Ancient Programme Cell Death Regulator - The Crystal Structure Of Marine Sponge Bhp2 Bound To Lb-Bak-2.
Cell Death Dis V. 8 E2543 2017
PubMed-ID: 28079890  |  Reference-DOI: 10.1038/CDDIS.2016.469

(-) Compounds

Molecule 1 - BCL-X HOMOLOGOUS PROTEIN, BHP2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 19-200
    Gene: BHP2
    Organism Common: SPONGE
    Organism Scientific: GEODIA CYDONIUM
    Organism Taxid: 6047
 
Molecule 2 - BAK-2 PROTEIN
    Chains: D, C
    Engineered: YES
    Fragment: UNP RESIDUES 64-88
    Organism Scientific: LUBOMIRSKIA BAICALENSIS
    Organism Taxid: 289074
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 22)

Asymmetric Unit (2, 22)
No.NameCountTypeFull Name
1B3P2Ligand/Ion2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2EDO20Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1B3P1Ligand/Ion2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2EDO10Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 11)
No.NameCountTypeFull Name
1B3P1Ligand/Ion2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2EDO10Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:129 , VAL A:131 , HIS A:132 , ARG A:135 , HOH A:409 , HOH A:460 , EDO D:101binding site for residue EDO A 301
02AC2SOFTWAREASP A:113 , HOH A:416 , GLU B:121 , ARG B:124 , ALA C:64 , HOH C:203binding site for residue EDO A 302
03AC3SOFTWARELEU A:23 , THR A:26 , GLU A:30 , HOH A:413binding site for residue EDO A 303
04AC4SOFTWAREGLU A:121 , ARG A:124 , HOH A:406 , ASP B:113 , ASN B:114 , HOH B:403 , ALA D:64binding site for residue EDO A 304
05AC5SOFTWAREGLU A:116 , TRP A:165 , GLN A:179 , ASN A:182 , GLY A:183 , HOH A:404 , HOH A:459binding site for residue EDO A 305
06AC6SOFTWAREASP A:172 , ASN A:182 , VAL A:189 , B3P A:309 , HOH A:407 , HOH A:443binding site for residue EDO A 306
07AC7SOFTWAREARG A:120 , GLU A:123 , SER A:173 , HOH A:443binding site for residue EDO A 307
08AC8SOFTWAREGLU A:123 , PHE A:127 , SER A:173 , LEU A:174 , HOH A:442binding site for residue EDO A 308
09AC9SOFTWARETRP A:133 , ARG A:168 , ASN A:171 , ASP A:172 , GLU A:181 , ASN A:182 , GLY A:186 , EDO A:306 , HOH A:424 , HOH A:428 , HOH A:439 , PHE D:86 , TYR D:87binding site for residue B3P A 309
10AD1SOFTWAREHIS A:132 , EDO A:301 , ASP D:83binding site for residue EDO D 101
11AD2SOFTWAREGLY A:93 , ASN A:99 , ARG D:74binding site for residue EDO D 102
12AD3SOFTWAREGLU B:181 , B3P B:309 , HOH B:423binding site for residue EDO B 301
13AD4SOFTWARESER A:152 , ARG B:104 , TYR B:149 , SER B:152 , ARG B:153 , HOH B:417binding site for residue EDO B 302
14AD5SOFTWAREARG B:125 , SER B:128 , ASP B:129 , ARG B:135 , HOH B:430 , ALA C:76 , GLU C:77 , ASP C:80binding site for residue EDO B 303
15AD6SOFTWAREGLY B:93 , ASN B:99 , ASP B:102 , HOH B:410 , ARG C:74 , LEU C:75binding site for residue EDO B 304
16AD7SOFTWARELEU B:23 , THR B:26 , GLU B:30binding site for residue EDO B 305
17AD8SOFTWAREPRO B:112 , ASP B:113 , ASN B:114 , VAL B:115 , GLU B:116 , SER B:117 , HOH B:403 , HOH B:418 , HOH B:454binding site for residue EDO B 306
18AD9SOFTWAREGLU B:123 , PHE B:127 , SER B:173 , HOH B:437binding site for residue EDO B 307
19AE1SOFTWAREGLY B:17 , ARG B:20 , LEU B:21 , GLN B:24 , GLU B:73 , GLN B:179binding site for residue EDO B 308
20AE2SOFTWARETYR B:22 , TRP B:133 , ARG B:168 , ASN B:171 , ASP B:172 , GLU B:181 , ASN B:182 , GLY B:186 , EDO B:301 , HOH B:431 , PHE C:86 , TYR C:87binding site for residue B3P B 309
21AE3SOFTWAREHIS B:132 , ASP C:80 , ASP C:83binding site for residue EDO C 101
22AE4SOFTWAREMET C:67 , GLU C:70 , HOH C:201binding site for residue EDO C 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5TWA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TWA)

(-) 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:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5twa A  14 GPLGSSRLYLQNTAVMEELYRRNLEYWREDGLSEEERRTAADAAERMTAVIAGTPGIAVERNVRDFRRGGWDVTPDNVESEFREVERRTFSDGVHWGRVIAFLAFSMSFAAYVNSRGIDGGAYSVFNWTLRVLNDSLADFIQRENGWRGFIVYADTLLRAQ 198
                                    23        33   ||   67        77        87        97       107       117       127       137       147       157       167       177       187       197 
                                                  37|  57|                                                                                                                                   
                                                   53   67                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5twa B  14 GPLGSSRLYLQNTAVMEELYRRNLSEYWRLSEEERRTAADAAERMTAVIAGTPGIAVERNVRDFRRGGWDVTPDNVESEFREVERRTFSDGVHWGRVIAFLAFSMSFAAYVNSRGIDGGAYSVFNWTLRVLNDSLADFIQRENGWRGFIVYADTLLRA 197
                                    23        33    ||  69        79        89        99       109       119       129       139       149       159       169       179       189        
                                                   38| 56|                                                                                                                                
                                                    53  69                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:25
                                                         
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                 5twa C  64 ASSMASEVGRRLAEFGDQVDGQFYQ  88
                                    73        83     


Chain D from PDB  Type:PROTEIN  Length:25
                                                         
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                 5twa D  64 ASSMASEVGRRLAEFGDQVDGQFYQ  88
                                    73        83
   Legend:   → Mismatch (orange background)
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  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 5TWA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 6)

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