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(-) Description

Title :  X-RAY STRUCTURE OF MACROPHAGE INFLAMMATORY PROTEIN-1 ALPHA (CCL3) N-TERMINAL-SWITCH POLYMER
 
Authors :  W. G. Liang, W. Tang
Date :  20 Jul 15  (Deposition) - 13 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,C,E,G,I  (1x)
Biol. Unit 2:  B,D,F,H,J  (1x)
Keywords :  Cc Chemokine, Ccl3, Oligomer, Signaling Protein, 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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - C-C MOTIF CHEMOKINE 3
    Chains: A, B, C, D, E, F, G, H, I, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (1x): A C E G I 
Biological Unit 2 (1x):  B D F H J

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2HEZ10Ligand/IonHEXANE-1,6-DIOL
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2HEZ6Ligand/IonHEXANE-1,6-DIOL
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2HEZ4Ligand/IonHEXANE-1,6-DIOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:28 , GLU A:30 , HEZ A:102 , VAL I:50binding site for residue HEZ A 101
02AC2SOFTWAREHEZ A:101 , SER I:47 , ARG I:48 , GLN I:49 , THR J:7binding site for residue HEZ A 102
03AC3SOFTWARETYR J:28 , GLU J:30binding site for residue HEZ B 101
04AC4SOFTWAREARG A:46 , GLN C:22 , ALA C:26 , TYR C:62 , ASP C:65 , LEU C:66binding site for residue HEZ C 101
05AC5SOFTWAREGLN E:19 , PRO E:21 , GLN E:22 , TYR E:62binding site for residue HEZ E 101
06AC6SOFTWAREARG E:18 , ARG E:48 , HOH E:206 , TYR G:28 , GLU G:30binding site for residue HEZ E 102
07AC7SOFTWAREARG C:18 , TYR E:28 , GLU E:30 , HOH E:216binding site for residue HEZ E 103
08AC8SOFTWARETYR F:28 , GLU F:30binding site for residue HEZ F 101
09AC9SOFTWAREGLN F:19 , GLU F:57 , LYS F:61binding site for residue ACT F 102
10AD1SOFTWAREGLN H:19 , GLN H:22 , ASN H:23 , TYR H:62 , SER I:55 , GLN I:60binding site for residue HEZ H 101
11AD2SOFTWARETYR H:28 , GLU H:30binding site for residue HEZ H 102
12AD3SOFTWAREPRO H:8 , SER I:2 , LEU I:3binding site for residue ACT I 101
13AD4SOFTWAREGLN I:19 , LYS I:61binding site for residue ACT I 102

(-) SS Bonds  (20, 20)

Asymmetric 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
11F:11 -F:35
12F:12 -F:51
13G:11 -G:35
14G:12 -G:51
15H:11 -H:35
16H:12 -H:51
17I:11 -I:35
18I:12 -I:51
19J:11 -J:35
20J:12 -J:51

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5COR)

(-) 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:70
                                                                                                     
               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
                  5cor A  1 ASLAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELSA 70
                                    10        20        30        40        50        60        70


Chain B from PDB  Type:PROTEIN  Length:68
                                                                                                   
               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
                  5cor B  3 LAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELSA 70
                                    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...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  5cor C  4 AADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELSA 70
                                    13        23        33        43        53        63       


Chain D from PDB  Type:PROTEIN  Length:68
                                                                                                   
               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
                  5cor D  3 LAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELSA 70
                                    12        22        32        42        52        62        


Chain E from PDB  Type:PROTEIN  Length:68
                                                                                                   
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  5cor E  3 LAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELSA 70
                                    12        22        32        42        52        62        


Chain F from PDB  Type:PROTEIN  Length:70
                                                                                                     
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  5cor F  1 ASLAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELSA 70
                                    10        20        30        40        50        60        70


Chain G from PDB  Type:PROTEIN  Length:70
                                                                                                     
               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
                  5cor G  1 ASLAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELSA 70
                                    10        20        30        40        50        60        70


Chain H from PDB  Type:PROTEIN  Length:68
                                                                                                   
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  5cor H  3 LAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELSA 70
                                    12        22        32        42        52        62        


Chain I 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...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  5cor I  2 SLAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELSA 70
                                    11        21        31        41        51        61         


Chain J from PDB  Type:PROTEIN  Length:70
                                                                                                     
               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
                  5cor J  1 ASLAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQKYVSDLELSA 70
                                    10        20        30        40        50        60        70
   Legend:   → Mismatch (orange background)
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    → 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 5COR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (70, 70)

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        CCL3_HUMAN | P10147: 1b50 1b53 2x69 2x6g 3fpu 3h44 3kbx 4ra8 4zkb 5d65

(-) Related Entries Specified in the PDB File

5d65