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(-) Description

Title :  CRYSTAL STRUCTURE OF CC CHEMOKINE 5 (CCL5) OLIGOMER IN COMPLEX WITH HEPARIN
 
Authors :  W. G. Liang, W. Tang
Date :  10 Sep 15  (Deposition) - 13 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I
Keywords :  Cc Chemokine, High Oligomer, 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 5
    Chains: A, B, C, D, E, F, G, H, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 27-91
    Gene: CCL5, D17S136E, SCYA5
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SERINE AT THE N-TERMINAL HAS O-LINKED GLYCOSYLATION BY GLUCOSE.
    Synonym: EOCP,EOSINOPHIL CHEMOTACTIC CYTOKINE,SIS-DELTA,SMALL- INDUCIBLE CYTOKINE A5,T CELL-SPECIFIC PROTEIN P228,TCP228,T-CELL- SPECIFIC PROTEIN RANTES

 Structural Features

(-) Chains, Units

  123456789
Asymmetric/Biological Unit : ABCDEFGHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 46)

Asymmetric/Biological Unit (7, 46)
No.NameCountTypeFull Name
1BGC5Ligand/IonBETA-D-GLUCOSE
2CL20Ligand/IonCHLORIDE ION
3GLA6Ligand/IonALPHA D-GALACTOSE
4IDS3Ligand/Ion2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
5SGN6Ligand/IonN,O6-DISULFO-GLUCOSAMINE
6SO45Ligand/IonSULFATE ION
7TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (37, 37)

Asymmetric Unit (37, 37)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:5 , ASP A:6 , THR A:8 , SER A:31 , GLA A:101 , HOH A:218 , SER D:5 , ASP D:6 , THR D:8 , SER D:31binding site for residue BGC A 102
02AC2SOFTWAREGLU A:54 , LYS A:55 , LYS A:56 , CL A:105binding site for residue SO4 A 103
03AC3SOFTWARESER A:35 , SER B:35binding site for residue CL A 104
04AC4SOFTWARESO4 A:103binding site for residue CL A 105
05AC5SOFTWAREARG B:21 , ILE B:24binding site for residue CL B 101
06AC6SOFTWARELYS B:56binding site for residue CL B 102
07AC7SOFTWARETYR B:27 , GLU B:66binding site for residue TRS B 103
08AC8SOFTWAREASP C:6 , THR C:8 , SER C:31 , LYS C:33 , ASP F:6 , THR F:8 , SER F:31binding site for residue BGC C 102
09AC9SOFTWARESER C:35 , SER D:35binding site for residue CL C 103
10AD1SOFTWAREARG C:21 , ILE C:24binding site for residue CL C 104
11AD2SOFTWAREARG C:59 , PRO E:20binding site for residue CL C 106
12AD3SOFTWAREILE D:24binding site for residue CL D 102
13AD4SOFTWAREGLU E:66 , TYR G:27 , GLU G:66binding site for residue BGC E 101
14AD5SOFTWARELYS E:55 , LYS E:56 , HOH E:201binding site for residue SO4 E 102
15AD6SOFTWAREARG E:21 , ILE E:24binding site for residue CL E 103
16AD7SOFTWARELYS F:55 , LYS F:56 , TRP F:57 , CL F:105binding site for residue SO4 F 102
17AD8SOFTWARESER E:35 , SER F:35binding site for residue CL F 103
18AD9SOFTWAREASN F:52binding site for residue CL F 104
19AE1SOFTWARELYS F:56 , SO4 F:102binding site for residue CL F 105
20AE2SOFTWAREGLU G:26 , GLN G:48 , HOH G:211binding site for residue BGC G 101
21AE3SOFTWARELYS G:55 , LYS G:56 , HOH G:215binding site for residue SO4 G 102
22AE4SOFTWAREARG G:21 , ILE G:24binding site for residue CL G 103
23AE5SOFTWAREMET G:67binding site for residue CL G 104
24AE6SOFTWAREASP H:6 , THR H:8 , SER H:31 , LYS H:33 , HOH H:202 , THR I:8 , SER I:31 , LYS I:33binding site for residue BGC H 102
25AE7SOFTWAREGLU H:54 , LYS H:55 , LYS H:56 , CL H:104binding site for residue SO4 H 103
26AE8SOFTWARETRP H:57 , SO4 H:103binding site for residue CL H 104
27AE9SOFTWARESER H:35binding site for residue CL H 105
28AF1SOFTWAREARG I:21 , ILE I:24 , HOH I:208binding site for residue CL I 102
29AF2SOFTWARESER A:4 , SER A:5 , BGC A:102 , HOH A:205 , PRO D:9 , GLU D:26 , PHE D:28binding site for Mono-Saccharide GLA A 101 bound to SER A 4
30AF3SOFTWARESER C:4 , SER C:5 , HOH C:206 , PRO F:9 , GLU F:26 , PHE F:28 , GLN F:48binding site for Mono-Saccharide GLA C 101 bound to SER C 4
31AF4SOFTWAREPRO A:9 , GLU A:26 , PHE A:28 , GLN A:48 , HOH A:218 , SER D:4 , HOH D:208 , HOH D:212binding site for Mono-Saccharide GLA D 101 bound to SER D 4
32AF5SOFTWAREPRO C:9 , PHE C:28 , SER F:4 , SER F:5 , HOH F:215binding site for Mono-Saccharide GLA F 101 bound to SER F 4
33AF6SOFTWARESER H:4 , SER H:5 , HOH H:206 , PRO I:9 , GLU I:26 , PHE I:28binding site for Mono-Saccharide GLA H 101 bound to SER H 4
34AF7SOFTWAREPRO H:9 , PHE H:28 , GLN H:48 , HOH H:202 , SER I:4 , SER I:5 , HOH I:207binding site for Mono-Saccharide GLA I 101 bound to SER I 4
35AF8SOFTWAREGLU C:54 , LYS C:55 , LYS C:56 , TRP C:57 , ARG C:59binding site for Poly-Saccharide residues SGN C 107 through SGN C 109
36AF9SOFTWAREARG C:21 , ILE C:24 , GLU C:54 , LYS C:55 , LYS C:56 , TRP C:57 , ARG C:59 , SGN C:107 , GLU D:54 , LYS D:55 , LYS D:56 , TRP D:57 , ARG D:59 , PRO E:20binding site for Poly-Saccharide residues SGN D 104 through SGN D 106
37AG1SOFTWAREGLU D:54 , LYS D:55 , LYS D:56 , TRP D:57 , ARG D:59 , GLU I:54 , LYS I:56 , TRP I:57 , ARG I:59 , GLU I:60binding site for Poly-Saccharide residues SGN I 104 through SGN I 106

(-) SS Bonds  (18, 18)

Asymmetric/Biological Unit
No.Residues
1A:10 -A:34
2A:11 -A:50
3B:10 -B:34
4B:11 -B:50
5C:10 -C:34
6C:11 -C:50
7D:10 -D:34
8D:11 -D:50
9E:10 -E:34
10E:11 -E:50
11F:10 -F:34
12F:11 -F:50
13G:10 -G:34
14G:11 -G:50
15H:10 -H:34
16H:11 -H:50
17I:10 -I:34
18I:11 -I:50

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DNF)

(-) 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:65
                                                                                                
               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
                  5dnf A  4 SSDTTPCCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYINSLEMS 68
                                    13        23        33        43        53        63     


Chain B from PDB  Type:PROTEIN  Length:65
                                                                                                
               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
                  5dnf B  4 SSDTTPCCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYINSLEMS 68
                                    13        23        33        43        53        63     


Chain C from PDB  Type:PROTEIN  Length:65
                                                                                                
               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
                  5dnf C  4 SSDTTPCCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYINSLEMS 68
                                    13        23        33        43        53        63     


Chain D from PDB  Type:PROTEIN  Length:65
                                                                                                
               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
                  5dnf D  4 SSDTTPCCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYINSLEMS 68
                                    13        23        33        43        53        63     


Chain E from PDB  Type:PROTEIN  Length:65
                                                                                                
               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
                  5dnf E  4 SSDTTPCCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYINSLEMS 68
                                    13        23        33        43        53        63     


Chain F from PDB  Type:PROTEIN  Length:65
                                                                                                
               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
                  5dnf F  4 SSDTTPCCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYINSLEMS 68
                                    13        23        33        43        53        63     


Chain G from PDB  Type:PROTEIN  Length:65
                                                                                                
               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
                  5dnf G  4 SSDTTPCCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYINSLEMS 68
                                    13        23        33        43        53        63     


Chain H from PDB  Type:PROTEIN  Length:65
                                                                                                
               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
                  5dnf H  4 SSDTTPCCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYINSLEMS 68
                                    13        23        33        43        53        63     


Chain I from PDB  Type:PROTEIN  Length:65
                                                                                                
               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
                  5dnf I  4 SSDTTPCCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYINSLEMS 68
                                    13        23        33        43        53        63
   Legend:   → Mismatch (orange background)
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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)

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(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (121, 121)

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UniProtKB/Swiss-Prot
        CCL5_HUMAN | P13501: 1b3a 1eqt 1hrj 1rtn 1rto 1u4l 1u4m 1u4p 1u4r 2l9h 2vxw 5cmd 5coy 5uiw

(-) Related Entries Specified in the PDB File

5cmd 5coy