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(-) Description

Title :  X-RAY STRUCTURE OF CA(2+)-S100B WITH HUMAN RAGE-DERIVED W72 PEPTIDE
 
Authors :  J. L. Jensen, C. L. Colbert
Date :  13 Aug 15  (Deposition) - 17 Aug 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B,P
Keywords :  Metal Binding Protein, Membrane Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. L. Jensen, C. L. Colbert
X-Ray Structure Of Ca(2+)-S100B With Human Rage-Derived W72 Peptide
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN S100-B
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEMEX-S100B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneS100B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymS-100 PROTEIN BETA CHAIN,S-100 PROTEIN SUBUNIT BETA,S100 CALCIUM-BINDING PROTEIN B
 
Molecule 2 - ADVANCED GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR
    ChainsP
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRECEPTOR FOR ADVANCED GLYCOSYLATION END PRODUCTS
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GOL6Ligand/IonGLYCEROL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:19 , GLU A:22 , ASP A:24 , LYS A:27 , GLU A:32 , HOH A:912binding site for residue CA A 801
02AC2SOFTWAREASP A:62 , ASP A:64 , ASP A:66 , GLU A:68 , GLU A:73 , HOH A:948binding site for residue CA A 802
03AC3SOFTWARELYS A:49 , GLU A:50 , GLY B:65 , ASP B:66binding site for residue GOL A 803
04AC4SOFTWAREMET A:80 , THR A:83 , HOH A:953 , HOH A:980 , HOH B:927binding site for residue GOL A 804
05AC5SOFTWAREGLU A:22 , GLY A:23 , GOL A:806 , HOH A:911binding site for residue GOL A 805
06AC6SOFTWAREGLY A:23 , GOL A:805 , HOH A:902 , HOH A:910 , HOH A:977binding site for residue GOL A 806
07AC7SOFTWARELYS A:30 , SER A:31 , LYS A:34 , GLN A:51 , VAL A:54 , HOH A:901 , HOH A:950 , HOH A:991 , HOH B:938binding site for residue GOL A 807
08AC8SOFTWARESER B:19 , GLU B:22 , ASP B:24 , LYS B:27 , GLU B:32 , HOH B:913binding site for residue CA B 801
09AC9SOFTWAREASP B:62 , ASP B:64 , ASP B:66 , GLU B:68 , GLU B:73 , HOH B:948binding site for residue CA B 802
10AD1SOFTWARELYS B:30 , SER B:31 , LYS B:34 , GLN B:51 , HOH B:903 , HOH B:947 , HOH B:964binding site for residue GOL B 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D7F)

(-) Cis Peptide Bonds  (1, 2)

Asymmetric/Biological Unit
No.Residues
1Gly P:1 -Pro P:2

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D7F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D7F)

(-) Exons   (0, 0)

(no "Exon" information available for 5D7F)

(-) 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:91
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  5d7f A  1 MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDNDGDGECDFQEFMAFVAMVTTACHEFFEH 91
                                    10        20        30        40        50        60        70        80        90 

Chain B from PDB  Type:PROTEIN  Length:91
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  5d7f B  1 MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDNDGDGECDFQEFMAFVAMVTTACHEFFEH 91
                                    10        20        30        40        50        60        70        80        90 

Chain P from PDB  Type:PROTEIN  Length:10
                                         
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  5d7f P  1 GPWDSVARVL 10
                                    10

   Legend:   → Mismatch (orange background)
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    → 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 5D7F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D7F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D7F)

(-) Gene Ontology  (101, 110)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAGE_HUMAN | Q151091pwi 2bjp 2e5e 2ens 2l7u 2le9 2lmb 2m1k 2mjw 2mov 3cjj 3o3u 4lp4 4lp5 4of5 4ofv 4oi7 4oi8 4p2y 4xyn 4ybh
        S100B_HUMAN | P042711mq1 1uwo 2h61 2m49 2pru 3czt 3d0y 3d10 3hcm 4xyn 5csf 5csi 5csj 5csn

(-) Related Entries Specified in the PDB File

4xyn 4XYN CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT RAGE- DERIVED PEPTIDE