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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MURINE CD44 HYALURONAN BINDING DOMAIN COMPLEX WITH A SMALL MOLECULE
 
Authors :  L. K. Liu, B. C. Finzel
Date :  11 Jun 15  (Deposition) - 29 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.31
Chains :  Asym./Biol. Unit :  A
Keywords :  Link Module, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. K. Liu, B. C. Finzel
Crystal Structure Of The Murine Cd44 Hyaluronan Binding Domain Complex With A Small Molecule
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CD44 ANTIGEN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 21-171
    Gene: CD44, LY-24
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: EXTRACELLULAR MATRIX RECEPTOR III,ECMR-III,GP90 LYMPHOCYTE HOMING/ADHESION RECEPTOR,HUTCH-I,HERMES ANTIGEN,HYALURONATE RECEPTOR, LYMPHOCYTE ANTIGEN 24,LY-24,PHAGOCYTIC GLYCOPROTEIN 1,PGP-1, PHAGOCYTIC GLYCOPROTEIN I,PGP-I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
168N1Ligand/Ion[(1S)-1,2,3,4-TETRAHYDROISOQUINOLIN-1-YL]METHANOL
26BT1Ligand/Ion[(1R)-1,2,3,4-TETRAHYDROISOQUINOLIN-1-YL]METHANOL
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4SO41Ligand/IonSULFATE ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:32 , ASN A:89 , CYS A:134 , THR A:135 , SER A:136 , ARG A:155 , ASP A:156 , HOH A:311 , HOH A:313binding site for residue DMS A 201
02AC2SOFTWAREARG A:33 , PHE A:38 , PHE A:60 , ASN A:125binding site for residue SO4 A 202
03AC3SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
04AC4SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
05AC5SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
06AC6SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
07AC7SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
08AC8SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
09AC9SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
10AD1SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
11AD2SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
12AD3SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
13AD4SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
14AD5SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
15AD6SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
16AD7SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
17AD8SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
18AD9SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
19AE1SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
20AE2SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
21AE3SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
22AE4SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
23AE5SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
24AE6SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204
25AE7SOFTWAREASN A:29 , VAL A:30 , HIS A:39 , GLU A:41 , ASP A:68 , VAL A:153 , ASN A:154 , ARG A:155 , HOH A:376 , HOH A:380 , HOH A:389binding site for residues 68N A 203 and 6BT A 204

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:32 -A:134
2A:57 -A:123
3A:81 -A:101

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BZE)

(-) 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:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..ee..eeeeee......hhhhhhhhhhhh.....hhhhhhhhhhh.......ee....eeeee......hhhhh.eeee.........eeeee.......ee..........eeeeeeeeeee....eeeeeee...hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5bze A  24 NQIDLNVTCRYAGVFHVEKNGRYSISRTEAADLCQAFNSTLPTMDQMKLALSKGFETCRYGFIEGNVVIPRIHPNAICAANHTGVYILVTSNTSHYDTYCFNASAPPEEDCTSVTDLPNSFDGPVTITIVNRDGTRYSKKGEYRTHQEDI 173
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
   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 5BZE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (41, 41)

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
        CD44_MOUSE | P15379: 2jcp 2jcq 2jcr 2zpy 4mrd 4mre 4mrf 4mrg 4mrh 4np2 4np3 5bzc 5bzf 5bzg 5bzh 5bzi 5bzj 5bzk 5bzl 5bzm 5bzn 5bzo 5bzp 5bzq 5bzr 5bzs 5bzt

(-) Related Entries Specified in the PDB File

5bzc 5bzf 5bzg 5bzh 5bzi 5bzj 5bzm 5bzn 5bzo 5bzp 5bzq 5bzr 5bzs 5bzt