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(-) Description

Title :  GASDERMIN-B C-TERMINAL DOMAIN CONTAINING THE POLYMORPHISM RESIDUES ARG299:SER306 FUSED TO MALTOSE BINDING PROTEIN
 
Authors :  K. Chao, O. Herzberg
Date :  01 Oct 16  (Deposition) - 01 Feb 17  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha Helices, Fusion Protein, C-Terminal Domain, 2 Snps, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. K. Chao, L. Kulakova, O. Herzberg
Human Gasdermin-B And Disease: Sulfatide Binding, Caspase Cleavage, And Structural Impact Of Asthma- And Ibs-Associated Polymorphism
Proc. Natl. Acad. Sci. Usa 2017
PubMed: search  |  Reference-DOI: 10.1073/PNAS.1616783114

(-) Compounds

Molecule 1 - SUGAR ABC TRANSPORTER SUBSTRATE-BINDING PROTEIN,GASDERMIN- B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMALX(E)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MALE, OO96_18925, GSDMB, GSDML, PP4052, PRO2521
    Organism Common: HUMAN
    Organism Scientific: ESCHERICHIA COLI, HOMO SAPIENS
    Organism Taxid: 562, 9606
    Synonym: GASDERMIN-LIKE PROTEIN

 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  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MAL2Ligand/IonMALTOSE
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MAL1Ligand/IonMALTOSE
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2MAL1Ligand/IonMALTOSE
3NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:12 , ASP A:14 , LYS A:15 , TRP A:62 , ALA A:63 , ASP A:65 , ARG A:66 , GLU A:111 , GLU A:153 , PRO A:154 , TYR A:155 , TRP A:340 , HOH A:1602 , HOH A:1622 , HOH A:1625 , HOH A:1649 , HOH A:1678binding site for residue MAL A 1501
2AC2SOFTWARELYS A:305 , LYS A:1267 , PHE A:1315 , ASN A:1316 , GLY A:1319 , HOH A:1665binding site for residue ACT A 1502
3AC3SOFTWAREGLN A:325 , GLY A:327 , GLU A:328 , HOH A:1660 , HOH A:1699 , HOH A:1760binding site for residue NA A 1503
4AC4SOFTWAREASN B:12 , ASP B:14 , LYS B:15 , TRP B:62 , ALA B:63 , ASP B:65 , ARG B:66 , GLU B:111 , GLU B:153 , PRO B:154 , TYR B:155 , TRP B:340 , HOH B:1611binding site for residue MAL B 1501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe B:1235 -Pro B:1236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TIB)

(-) 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:533
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....hhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh......eeeee..hhhhhhhh........hhhhhh..hhhhhhhhee..ee..eeeeee..eeeee............hhhhhhhhhhhh..eee.....hhhhhhhhhhhh..eeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeehhhhhhhhhhh...eeee...ee..ee...eeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhhhhhee....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tib A    1 KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAAMSAGLDIHFRGKTKSRNMKEKLEDMESVLKDLTEEKRKDVLNSLAKCLGKEDIRQDLEQRVSEVLISRELHMEDSDKPLLSSLFNAAGVLVEARAKAILDFLDALLELSEEQQFVAEALEKGTLPLLKDQVKSVMEQNWDPEARILCALYVVVSILLELAEGP 1406
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370|     1229   || 1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1383      1393      1403   
                                                                                                                                                                                                                                                                                                                                                                                                           370|         1233|                                                                                                                        1370|                       
                                                                                                                                                                                                                                                                                                                                                                                                           1220          1246                                                                                                                         1383                       


Chain B from PDB  Type:PROTEIN  Length:530
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhh.....eeeee..hhhhhhhh........hhhhhh..hhhhhhhhee..ee..eeeeee..eeeee............hhhhhhhhhhhh..eee.....hhhhhhhhhhhh..eeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeehhhhhhhhhhh...eeee............eeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tib B    3 EEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAAMSAGLDIHFRGKTKSFPERNMKEKLEDMESVLKDLTEEKRKDVLNSLAKCLGKEDIRQDLEQRVSEVLISRELHMEDSDKPLLSSLFNAAGVLVEARAKAILDFLDALLELSEEQQFVAEALEKGTLPLLKDQVKSVMEDPEARILCALYVVVSILLELAEG 1405
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362      1221      1231     |1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1385      1395      1405
                                                                                                                                                                                                                                                                                                                                                                                                         370|             1237|                                                                                                                    1367|                      
                                                                                                                                                                                                                                                                                                                                                                                                         1220              1247                                                                                                                     1383
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  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 5TIB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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