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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF RACEMIC NON-GLYCOSYLATED CHEMOKINE SER-CCL1
 
Authors :  R. Okamoto, K. Mandal, M. R. Sawaya, Y. Kajihara, T. O. Yeates, S. B. H. Ke
Date :  19 Jan 14  (Deposition) - 07 May 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Chemical Protein Synthesis, Racemic Protein Crystallography, Glycoprotein, Chemokine, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Okamoto, K. Mandal, M. R. Sawaya, Y. Kajihara, T. O. Yeates, S. B. Ken
(Quasi-)Racemic X-Ray Structures Of Glycosylated And Non-Glycosylated Forms Of The Chemokine Ser-Ccl1 Prepared B Total Chemical Synthesis.
Angew. Chem. Int. Ed. Engl. V. 53 5194 2014
PubMed-ID: 24692304  |  Reference-DOI: 10.1002/ANIE.201400679

(-) Compounds

Molecule 1 - C-C MOTIF CHEMOKINE 1
    Chains: A, B
    Engineered: YES
    Fragment: UNP RESIDUES 23-96
    Synonym: SMALL-INDUCIBLE CYTOKINE A1, T LYMPHOCYTE-SECRETED PROTEIN I-309
    Synthetic: YES
 
Molecule 2 - D-SER-CCL1
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (20, 161)

Asymmetric Unit (20, 161)
No.NameCountTypeFull Name
1DAL8Mod. Amino AcidD-ALANINE
2DAR16Mod. Amino AcidD-ARGININE
3DAS2Mod. Amino AcidD-ASPARTIC ACID
4DCY12Mod. Amino AcidD-CYSTEINE
5DGL8Mod. Amino AcidD-GLUTAMIC ACID
6DGN4Mod. Amino AcidD-GLUTAMINE
7DHI4Mod. Amino AcidD-HISTIDINE
8DIL8Mod. Amino AcidD-ISOLEUCINE
9DLE12Mod. Amino AcidD-LEUCINE
10DLY10Mod. Amino AcidD-LYSINE
11DPN8Mod. Amino AcidD-PHENYLALANINE
12DPR6Mod. Amino AcidD-PROLINE
13DSG4Mod. Amino AcidD-ASPARAGINE
14DSN12Mod. Amino AcidD-SERINE
15DTH4Mod. Amino AcidD-THREONINE
16DTR2Mod. Amino AcidD-TRYPTOPHAN
17DTY2Mod. Amino AcidD-TYROSINE
18DVA6Mod. Amino AcidD-VALINE
19MED2Mod. Amino AcidD-METHIONINE
20SO431Ligand/IonSULFATE ION
Biological Unit 1 (1, 17)
No.NameCountTypeFull Name
1DAL-1Mod. Amino AcidD-ALANINE
2DAR-1Mod. Amino AcidD-ARGININE
3DAS-1Mod. Amino AcidD-ASPARTIC ACID
4DCY-1Mod. Amino AcidD-CYSTEINE
5DGL-1Mod. Amino AcidD-GLUTAMIC ACID
6DGN-1Mod. Amino AcidD-GLUTAMINE
7DHI-1Mod. Amino AcidD-HISTIDINE
8DIL-1Mod. Amino AcidD-ISOLEUCINE
9DLE-1Mod. Amino AcidD-LEUCINE
10DLY-1Mod. Amino AcidD-LYSINE
11DPN-1Mod. Amino AcidD-PHENYLALANINE
12DPR-1Mod. Amino AcidD-PROLINE
13DSG-1Mod. Amino AcidD-ASPARAGINE
14DSN-1Mod. Amino AcidD-SERINE
15DTH-1Mod. Amino AcidD-THREONINE
16DTR-1Mod. Amino AcidD-TRYPTOPHAN
17DTY-1Mod. Amino AcidD-TYROSINE
18DVA-1Mod. Amino AcidD-VALINE
19MED-1Mod. Amino AcidD-METHIONINE
20SO417Ligand/IonSULFATE ION
Biological Unit 2 (20, 144)
No.NameCountTypeFull Name
1DAL8Mod. Amino AcidD-ALANINE
2DAR16Mod. Amino AcidD-ARGININE
3DAS2Mod. Amino AcidD-ASPARTIC ACID
4DCY12Mod. Amino AcidD-CYSTEINE
5DGL8Mod. Amino AcidD-GLUTAMIC ACID
6DGN4Mod. Amino AcidD-GLUTAMINE
7DHI4Mod. Amino AcidD-HISTIDINE
8DIL8Mod. Amino AcidD-ISOLEUCINE
9DLE12Mod. Amino AcidD-LEUCINE
10DLY10Mod. Amino AcidD-LYSINE
11DPN8Mod. Amino AcidD-PHENYLALANINE
12DPR6Mod. Amino AcidD-PROLINE
13DSG4Mod. Amino AcidD-ASPARAGINE
14DSN12Mod. Amino AcidD-SERINE
15DTH4Mod. Amino AcidD-THREONINE
16DTR2Mod. Amino AcidD-TRYPTOPHAN
17DTY2Mod. Amino AcidD-TYROSINE
18DVA6Mod. Amino AcidD-VALINE
19MED2Mod. Amino AcidD-METHIONINE
20SO414Ligand/IonSULFATE ION

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01NC6SOFTWARESER A:32 , SER A:33 , HOH A:211 , HOH A:216BINDING SITE FOR RESIDUE SO4 A 101
02NC7SOFTWAREGLY A:57 , TRP A:58 , ARG A:61 , SO4 A:107 , HOH A:224BINDING SITE FOR RESIDUE SO4 A 102
03NC8SOFTWAREARG A:10 , ARG A:29 , SER A:71 , HOH A:228BINDING SITE FOR RESIDUE SO4 A 103
04NC9SOFTWAREPHE A:8 , ARG A:10 , HOH A:217 , PHE B:8 , ARG B:10 , SO4 B:102BINDING SITE FOR RESIDUE SO4 A 104
05OC1SOFTWAREARG A:29 , ASN A:30 , HIS A:68 , HOH A:229BINDING SITE FOR RESIDUE SO4 A 105
06OC2SOFTWAREARG A:67 , HIS A:68 , HOH A:226BINDING SITE FOR RESIDUE SO4 A 106
07OC3SOFTWARETHR A:55 , VAL A:56 , GLY A:57 , SO4 A:102 , HOH A:224 , DSN D:33BINDING SITE FOR RESIDUE SO4 A 107
08OC4SOFTWARESER A:36 , GLU A:38BINDING SITE FOR RESIDUE SO4 A 108
09OC5SOFTWAREGLU A:19 , ARG A:61 , HIS A:62 , HOH A:218 , HOH A:235BINDING SITE FOR RESIDUE SO4 A 109
10OC6SOFTWAREDAR C:67 , DAR D:67BINDING SITE FOR RESIDUE SO4 B 101
11OC7SOFTWARESO4 A:104 , ARG B:10 , ARG B:29 , PRO B:70 , SER B:71 , SO4 B:103 , DAR D:67BINDING SITE FOR RESIDUE SO4 B 102
12OC8SOFTWAREARG B:10 , ARG B:29 , SER B:71 , SO4 B:102BINDING SITE FOR RESIDUE SO4 B 103
13OC9SOFTWARESER B:32 , SER B:33 , HOH B:211BINDING SITE FOR RESIDUE SO4 B 104
14PC1SOFTWAREGLY B:57 , TRP B:58 , ARG B:61 , HOH C:208BINDING SITE FOR RESIDUE SO4 B 105
15PC2SOFTWAREARG B:67 , HIS B:68 , HOH B:225BINDING SITE FOR RESIDUE SO4 B 106
16PC3SOFTWARESER B:36 , GLU B:38 , HOH B:217BINDING SITE FOR RESIDUE SO4 B 107
17PC4SOFTWAREGLU B:19 , ARG B:61 , HIS B:62 , HOH B:224 , HOH B:228BINDING SITE FOR RESIDUE SO4 B 108
18PC5SOFTWAREARG A:67 , ARG B:67 , DLY C:72 , SO4 C:104 , DLY D:72BINDING SITE FOR RESIDUE SO4 C 101
19PC6SOFTWAREDSN C:32 , DSN C:33 , HOH C:222BINDING SITE FOR RESIDUE SO4 C 102
20PC7SOFTWAREDVA C:56 , GLY C:57 , DTR C:58 , DAR C:61 , HOH C:212 , HOH C:214BINDING SITE FOR RESIDUE SO4 C 103
21PC8SOFTWAREARG A:67 , DAR C:10 , DSN C:71 , DLY C:72 , SO4 C:101BINDING SITE FOR RESIDUE SO4 C 104
22PC9SOFTWAREDGL C:19 , DAR C:61 , DHI C:62BINDING SITE FOR RESIDUE SO4 C 105
23QC1SOFTWAREDAR C:10 , DAR C:29 , DSG C:30 , DHI C:68 , HOH C:223BINDING SITE FOR RESIDUE SO4 C 106
24QC2SOFTWAREDAR C:73BINDING SITE FOR RESIDUE SO4 C 107
25QC3SOFTWAREARG B:67 , DAR D:10 , DSN D:71 , DLY D:72 , SO4 D:102BINDING SITE FOR RESIDUE SO4 D 101
26QC4SOFTWAREDPN C:8 , DAR C:10 , DAR C:29 , DPN D:8 , DAR D:10 , DAR D:29 , SO4 D:101 , HOH D:224 , HOH D:228BINDING SITE FOR RESIDUE SO4 D 102
27QC5SOFTWAREDAR D:29 , DSG D:30 , DHI D:68BINDING SITE FOR RESIDUE SO4 D 103
28QC6SOFTWARESER A:33 , SER A:36 , DVA D:56 , GLY D:57 , DTR D:58 , DAR D:61BINDING SITE FOR RESIDUE SO4 D 104
29QC7SOFTWAREDGL D:19 , DAR D:61 , DHI D:62BINDING SITE FOR RESIDUE SO4 D 105
30QC8SOFTWAREDAR D:10 , DSN D:32 , DSN D:33BINDING SITE FOR RESIDUE SO4 D 106
31QC9SOFTWAREDAR D:73BINDING SITE FOR RESIDUE SO4 D 107

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:11 -A:35
2A:12 -A:51
3A:27 -A:69
4B:11 -B:35
5B:12 -B:51
6B:27 -B:69
7C:11 -C:35
8C:12 -C:51
9C:27 -C:69
10D:11 -D:35
11D:12 -D:51
12D:27 -D:69

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OIJ)

(-) 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:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.........hhh.eeeeee.hhhhh..eeeeee....eeeee..hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4oij A  4 MQVPFSRCCFSFAEQEIPLRAILCYRNTSSICSNEGLIFKLKRGKEACALDTVGWVQRHRKMLRHCPSKRK 74
                                    13        23        33        43        53        63        73 


Chain B from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.........hhh.eeeeee.hhhhh..eeeeee....eeeee..hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4oij B  4 MQVPFSRCCFSFAEQEIPLRAILCYRNTSSICSNEGLIFKLKRGKEACALDTVGWVQRHRKMLRHCPSKRK 74
                                    13        23        33        43        53        63        73 


Chain C from PDB  Type:PROTEIN  Length:68
                                                                                                   
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.........hhh.eeeee..hhhhh..eeeeee....eeeee..hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  4oij C  6 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGxxxxxxxGxxxxxxxxxGxxxxxxxxxxxxxxxx 73
                            ||||||||15||||||||25||||||||35||| ||||45| ||||||55| ||||||65||||||||
                            6-DVA|||15-DPN|||24-DAL|||33-DSN| ||43-DLY||||53-DLE||||63-DAR|||72-DLY
                             7-DPR|||16-DAL|||25-DIL|||34-DIL |||44-DLE||||54-DAS||||64-DLY|||73-DAR
                              8-DPN|| 17-DGL|| 26-DLE|| 35-DCY||| 45-DLY||| 55-DTH||| 65-MED||  
                               9-DSN|  18-DGN|  27-DCY|  36-DSN||  46-DAR||  56-DVA||  66-DLE|  
                               10-DAR   19-DGL   28-DTY   37-DSG|    48-DLY    58-DTR   67-DAR  
                                11-DCY   20-DIL   29-DAR   38-DGL     49-DGL    59-DVA   68-DHI 
                                 12-DCY   21-DPR   30-DSG    40-DLE    50-DAL    60-DGN   69-DCY
                                  13-DPN   22-DLE   31-DTH    41-DIL    51-DCY    61-DAR   70-DPR
                                   14-DSN   23-DAR   32-DSN    42-DPN    52-DAL    62-DHI   71-DSN


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.eeeee..hhhhh..eeeeee....eeeee..hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  4oij D  6 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGxxxxxxxGxxxxxxxxxGxxxxxxxxxxxxxxxx 73
                            ||||||||15||||||||25||||||||35||| ||||45| ||||||55| ||||||65||||||||
                            |||||||14-DSN|||23-DAR|||32-DSN|| |42-DPN |||52-DAL |||62-DHI|||71-DSN
                            6-DVA|||15-DPN|||24-DAL|||33-DSN| ||43-DLY||||53-DLE||||63-DAR|||72-DLY
                             7-DPR|| 16-DAL|| 25-DIL|| 34-DIL || 44-DLE||| 54-DAS||| 64-DLY|| 73-DAR
                              8-DPN|  17-DGL|  26-DLE|  35-DCY||  45-DLY||  55-DTH||  65-MED|   
                               9-DSN   18-DGN   27-DCY   36-DSN|   46-DAR|   56-DVA|   66-DLE   
                               10-DAR   19-DGL   28-DTY   37-DSG     48-DLY    58-DTR   67-DAR  
                                11-DCY   20-DIL   29-DAR   38-DGL     49-DGL    59-DVA   68-DHI 
                                 12-DCY   21-DPR   30-DSG    40-DLE    50-DAL    60-DGN   69-DCY
                                  13-DPN   22-DLE   31-DTH    41-DIL    51-DCY    61-DAR   70-DPR
   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)

(no "SCOP Domain" information available for 4OIJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

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  CCL1_HUMAN | P22362
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CCL1_HUMAN | P22362: 1el0 4oik

(-) Related Entries Specified in the PDB File

4oik