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(-) Description

Title :  HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE HUMAN CD44 HYALURONAN BINDING DOMAIN IN NEW SPACE GROUP
 
Authors :  L. K. Liu, B. Finzel
Date :  28 Mar 14  (Deposition) - 17 Sep 14  (Release) - 15 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Link Module, Binding Protein, Hyaluronan, Ectodomain, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. K. Liu, B. Finzel
High-Resolution Crystal Structures Of Alternate Forms Of Th Human Cd44 Hyaluronan-Binding Domain Reveal A Site For Protein Interaction.
Acta Crystallogr F Struct V. 70 1155 2014 Biol Commun
PubMed-ID: 25195884  |  Reference-DOI: 10.1107/S2053230X14015532

(-) Compounds

Molecule 1 - CD44 ANTIGEN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 18-171
    Gene: CD44, CD44 LY-24, LHR, MDU2, MDU3, MIC4
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CDW44, EPICAN, EXTRACELLULAR MATRIX RECEPTOR III, ECMR-III, GP90 LYMPHOCYTE HOMING/ADHESION RECEPTOR, HUTCH-I, HEPARAN SULFATE PROTEOGLYCAN, HERMES ANTIGEN, HYALURONATE RECEPTOR, PHAGOCYTIC GLYCOPROTEIN 1, PGP-1, PHAGOCYTIC GLYCOPROTEIN I, PGP-I

 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  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5SO46Ligand/IonSULFATE ION
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1DMS-1Ligand/IonDIMETHYL SULFOXIDE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5SO43Ligand/IonSULFATE ION
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL-1Ligand/IonGLYCEROL
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5SO43Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:41 , TYR A:42 , ARG A:78 , PEG A:204 , HOH A:307 , HOH A:310 , CYS B:77 , ARG B:78 , PEG B:203BINDING SITE FOR RESIDUE SO4 A 201
02AC2SOFTWAREARG A:29 , PHE A:34 , PHE A:56 , ASN A:120 , VAL A:132BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWAREALA A:31 , ASN A:120 , ALA A:123 , PRO A:125BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWARETYR A:42 , THR A:111 , GLN A:113 , TYR A:114 , SO4 A:201 , HOH A:407 , ASN B:94BINDING SITE FOR RESIDUE PEG A 204
05AC5SOFTWARETHR A:62 , ALA A:64 , GLN A:65 , HOH A:357 , HOH A:382 , HOH A:390 , HOH A:399 , ASP B:140 , GLY B:141BINDING SITE FOR RESIDUE GOL A 205
06AC6SOFTWARETHR A:27 , CYS A:28 , HOH A:375 , HOH A:394 , HOH A:411BINDING SITE FOR RESIDUE EDO A 206
07AC7SOFTWAREASN A:94 , ILE A:96 , SO4 B:201 , HOH B:355BINDING SITE FOR RESIDUE EDO A 207
08AC8SOFTWAREASP A:23 , ASN A:25 , ASN A:39 , GLY A:40 , ASP B:23 , ASN B:25 , GLY B:40BINDING SITE FOR RESIDUE PEG A 208
09AC9SOFTWARECYS A:77 , EDO A:207 , ARG B:41 , TYR B:42 , ARG B:78 , PEG B:203 , HOH B:315 , HOH B:325BINDING SITE FOR RESIDUE SO4 B 201
10BC1SOFTWAREARG B:46 , GLU B:83 , GLY B:84 , PEG B:208 , HOH B:349 , HOH B:380BINDING SITE FOR RESIDUE SO4 B 202
11BC2SOFTWAREGLU A:37 , GLY A:40 , ARG A:41 , ARG A:78 , SO4 A:201 , GLU B:37 , GLY B:40 , ARG B:41 , ARG B:78 , SO4 B:201 , HOH B:368BINDING SITE FOR RESIDUE PEG B 203
12BC3SOFTWAREARG B:29 , PHE B:56 , SER B:58 , ASN B:120 , VAL B:132BINDING SITE FOR RESIDUE SO4 B 204
13BC4SOFTWAREALA B:138 , PHE B:139 , GLN B:157 , LYS B:158BINDING SITE FOR RESIDUE EDO B 205
14BC5SOFTWAREALA B:20 , ILE B:143 , ARG B:162 , HOH B:322 , HOH B:323BINDING SITE FOR RESIDUE EDO B 206
15BC6SOFTWARESER A:95 , ILE A:96 , TYR B:79 , HOH B:372BINDING SITE FOR RESIDUE DMS B 207
16BC7SOFTWAREARG B:46 , HIS B:85 , VAL B:86 , SER B:109 , SO4 B:202 , HOH B:304 , HOH B:380BINDING SITE FOR RESIDUE PEG B 208

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:28 -A:129
2A:53 -A:118
3A:77 -A:97
4B:28 -B:129
5B:53 -B:118
6B:77 -B:97

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PZ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PZ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PZ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4PZ4)

(-) 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:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..ee..eeeeee......hhhhhhhhhhhh.....hhhhhhhhhhh.......eee..eeeeee......hhhhh.eeeee.......eeeee.......ee..........eeeeeeeeeee....eeeeeee...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pz4 A  18 AMAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPS 171
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167    


Chain B from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..ee..eeeeee......hhhhhhhhhhhh.....hhhhhhhhhhh.......eee..eeeeee......hhhhh.eeee........eeeee.......ee..........eeeeeeeeee.....eeeeeee...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pz4 B  20 AQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPS 171
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169
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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 4PZ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PZ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PZ4)

(-) Gene Ontology  (35, 35)

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 Related Entries

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        CD44_HUMAN | P16070: 1poz 1uuh 2i83 4pz3

(-) Related Entries Specified in the PDB File

1uuh APO HUMAN CD44 HABD 20-178
4pz3