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(-) Description

Title :  X-RAY STRUCTURE OF MACROPHAGE INFLAMMATORY PROTEIN-1 ALPHA (CCL3) WITH HEPARIN COMPLEX
 
Authors :  W. G. Liang, D. Y. Hwang, M. M. Zulueta, S. C. Hung, W. Tang
Date :  11 Aug 15  (Deposition) - 20 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Cc Chemokine, Ccl3, Oligomer, Signaling Protein, Heparin, Gag, Complex, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. G. Liang, C. G. Triandafillou, T. Y. Huang, M. M. Zulueta, S. Banerjee, A. R. Dinner, S. C. Hung, W. J. Tang
Structural Basis For Oligomerization And Glycosaminoglycan Binding Of Ccl5 And Ccl3.
Proc. Natl. Acad. Sci. Usa V. 113 5000 2016
PubMed-ID: 27091995  |  Reference-DOI: 10.1073/PNAS.1523981113

(-) Compounds

Molecule 1 - C-C MOTIF CHEMOKINE 3
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 23-92
    Gene: CCL3, G0S19-1, MIP1A, SCYA3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: G0/G1 SWITCH REGULATORY PROTEIN 19-1,MACROPHAGE INFLAMMATORY PROTEIN 1-ALPHA,MIP-1-ALPHA,PAT 464.1,SIS-BETA,SMALL-INDUCIBLE CYTOKINE A3,TONSILLAR LYMPHOCYTE LD78 ALPHA PROTEIN

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
1BGC9Ligand/IonBETA-D-GLUCOSE
2CL2Ligand/IonCHLORIDE ION
3GLC1Ligand/IonALPHA-D-GLUCOSE
4IDS2Ligand/Ion2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
5SGN2Ligand/IonN,O6-DISULFO-GLUCOSAMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:25 , ALA A:26 , SER A:69 , ARG B:46binding site for residue BGC A 101
02AC2SOFTWAREGLN A:34 , PRO A:38 , ASP A:53 , BGC A:103 , TYR B:15 , LYS B:37binding site for residue BGC A 102
03AC3SOFTWAREASP A:53 , SER A:55 , BGC A:102 , SER B:36 , LYS B:37 , GLC E:101binding site for residue BGC A 103
04AC4SOFTWAREGLN A:19 , LYS A:61binding site for residue BGC A 104
05AC5SOFTWAREGLN A:60 , PRO B:21 , SER B:55 , GLU B:57 , GLN B:60binding site for residue BGC B 101
06AC6SOFTWARESER B:36 , SER C:36binding site for residue CL B 102
07AC7SOFTWAREGLN C:22 , ILE C:25 , LYS C:45 , LEU C:66binding site for residue BGC C 101
08AC8SOFTWARETHR B:7 , THR B:9 , SER B:32 , GLN B:34 , SER C:14 , ASP D:6 , THR D:7 , THR D:9 , GLN D:34 , SER E:14binding site for residue BGC D 101
09AC9SOFTWAREARG D:18 , GLU E:30 , GLN E:60 , VAL E:63binding site for residue BGC D 102
10AD1SOFTWAREGLU A:57 , BGC A:103 , SER B:33 , CYS B:35 , PRO B:38 , SER E:17 , ARG E:18binding site for residue GLC E 101
11AD2SOFTWAREGLN E:19binding site for residue BGC E 102
12AD3SOFTWARESER D:36 , SER E:36binding site for residue CL E 103
13AD4SOFTWAREGLN B:22 , ALA B:26 , LYS B:45 , SGN B:105 , ARG E:46binding site for Poly-Saccharide residues SGN B 103 through IDS B 104
14AD5SOFTWAREGLN B:19 , GLN B:22 , ASN B:23 , GLU B:57 , TRP B:58 , LYS B:61 , ASP B:65 , IDS B:104binding site for Poly-Saccharide residues SGN B 105 through IDS B 106

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:11 -A:35
2A:12 -A:51
3B:11 -B:35
4B:12 -B:51
5C:11 -C:35
6C:12 -C:51
7D:11 -D:35
8D:12 -D:51
9E:11 -E:35
10E:12 -E:51

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D65)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D65)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D65)

(-) Exons   (0, 0)

(no "Exon" information available for 5D65)

(-) 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 ...................hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  5d65 A  2 SLAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELS 69
                                    11        21        31        41        51        61        


Chain B from PDB  Type:PROTEIN  Length:67
                                                                                                  
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  5d65 B  3 LAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELS 69
                                    12        22        32        42        52        62       


Chain C from PDB  Type:PROTEIN  Length:67
                                                                                                  
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  5d65 C  3 LAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELS 69
                                    12        22        32        42        52        62       


Chain D from PDB  Type:PROTEIN  Length:67
                                                                                                  
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  5d65 D  3 LAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELS 69
                                    12        22        32        42        52        62       


Chain E from PDB  Type:PROTEIN  Length:69
                                                                                                    
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.........hhh.eeeeee.........eeeee....eeee....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  5d65 E  1 ASLAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELS 69
                                    10        20        30        40        50        60
   Legend:   → Mismatch (orange background)
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  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 5D65)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D65)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D65)

(-) Gene Ontology  (70, 70)

Asymmetric/Biological Unit(hide GO term definitions)

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        CCL3_HUMAN | P10147: 1b50 1b53 2x69 2x6g 3fpu 3h44 3kbx 4ra8 4zkb 5cor

(-) Related Entries Specified in the PDB File

5cmd 5cor 5coy 5dnf