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(-) Description

Title :  CRYSTAL STRUCTURE OF CXCL12 IN COMPLEX WITH INHIBITOR
 
Authors :  E. W. Smith, Y. Chen
Date :  09 Aug 14  (Deposition) - 12 Nov 14  (Release) - 03 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cxcl12, Inhibitor, Complex, Chemokine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. W. Smith, Y. Liu, A. E. Getschman, F. C. Peterson, J. J. Ziarek, R. Li, B. F. Volkman, Y. Chen
Structural Analysis Of A Novel Small Molecule Ligand Bound To The Cxcl12 Chemokine.
J. Med. Chem. V. 57 9693 2014
PubMed-ID: 25356720  |  Reference-DOI: 10.1021/JM501194P

(-) Compounds

Molecule 1 - STROMAL CELL-DERIVED FACTOR 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 22-89
    Gene: CXCL12, SDF1, SDF1A, SDF1B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HSDF-1,C-X-C MOTIF CHEMOKINE 12,INTERCRINE REDUCED IN HEPATOMAS,HIRH,PRE-B CELL GROWTH-STIMULATING FACTOR,PBSF

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
13GG1Ligand/Ion1-PHENYL-3-[4-(1H-TETRAZOL-5-YL)PHENYL]UREA
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:8 , GLU A:15 , ALA A:19 , ASN A:22 , LEU A:42 , ASN A:45 , ARG A:47 , VAL A:49binding site for residue 3GG A 101
2AC2SOFTWAREPRO A:2 , VAL A:3 , SER A:4 , ALA A:19 , ARG A:20 , ALA A:21 , HOH A:201binding site for residue SO4 A 102
3AC3SOFTWAREARG B:41 , ARG B:47 , GLN B:48binding site for residue SO4 B 101

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:9 -A:34
2A:11 -A:50
3B:9 -B:34
4B:11 -B:50

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UAI)

(-) 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:68
                                                                                                   
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh............hhh.eeeeeee........eeeee.....eee......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  4uai A  1 KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNK 68
                                    10        20        30        40        50        60        


Chain B from PDB  Type:PROTEIN  Length:67
                                                                                                  
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhh.eeeeeee........eeeee.....eee....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  4uai B  2 PVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNK 68
                                    11        21        31        41        51        61
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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 4UAI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (50, 50)

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
        SDF1_HUMAN | P48061: 1a15 1qg7 1sdf 1vmc 2j7z 2k01 2k03 2k04 2k05 2kec 2ked 2kee 2kol 2n55 2nwg 2sdf 3gv3 3hp3 4lmq

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