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(-) Description

Title :  CRYSTAL STRUCTURE OF MACROPHAGE MIGRATION INHIBITORY FACTOR FROM PLASMODIUM BERGHEI
 
Authors :  S. E. Dobson, K. D. Augustijn, J. A. Brannigan, E. J. Dodson, A. P. Waters, A. J. Wilkinson
Date :  08 Jun 09  (Deposition) - 27 Oct 09  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  D,E,F  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. E. Dobson, K. D. Augustijn, J. A. Brannigan, C. Schnick, C. J. Janse, E. J. Dodson, A. P. Waters, A. J. Wilkinson
The Crystal Structures Of Macrophage Migration Inhibition Factor (Mif) From Plasmodium Falciparum And Plasmodium Berghei.
Protein Sci. V. 18 2578 2009
PubMed-ID: 19827093  |  Reference-DOI: 10.1002/PRO.263

(-) Compounds

Molecule 1 - MACROPHAGE MIGRATION INHIBITORY FACTOR
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-70
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 2-116
    Organism Scientific: PLASMODIUM BERGHEI
    Organism Taxid: 5823
    Other Details: CYS2 IS MODIFIED TO CME IN ALL CHAINS DUE TO BINDING TO BETA-MERCAPTOETHANOL
    Strain: ANKA

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x):    DEF
Biological Unit 2 (1x): ABC   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1CME6Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2GOL8Ligand/IonGLYCEROL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CME3Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2GOL3Ligand/IonGLYCEROL
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1CME3Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2GOL5Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:8 , LYS A:46 , ASN A:54 , GLY A:56 , HOH A:2034BINDING SITE FOR RESIDUE GOL A1116
2AC2SOFTWAREGLU A:55 , GLY A:56 , LYS A:91 , ARG A:94 , HOH A:2068BINDING SITE FOR RESIDUE GOL A1117
3AC3SOFTWAREHOH B:2008BINDING SITE FOR RESIDUE GOL B1115
4AC4SOFTWAREILE B:68 , ASN B:73 , PHE B:99 , ARG B:100 , ASP B:101 , HOH B:2093 , HOH B:2100 , HOH B:2101 , PHE C:107BINDING SITE FOR RESIDUE GOL B1116
5AC5SOFTWAREASN C:8 , LYS C:46 , ASN C:54 , HOH C:2041BINDING SITE FOR RESIDUE GOL C1116
6AC6SOFTWAREASN D:8 , LYS D:46 , ASN D:54 , HOH D:2036BINDING SITE FOR RESIDUE GOL D1116
7AC7SOFTWAREARG E:70 , ASN E:73 , HOH E:2060 , HOH E:2085 , PHE F:107 , PHE F:109BINDING SITE FOR RESIDUE GOL E1117
8AC8SOFTWAREASN F:8 , LYS F:46 , ASN F:54 , HOH F:2088BINDING SITE FOR RESIDUE GOL F1116

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WKB)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly C:66 -Gly C:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WKB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WKB)

(-) Exons   (0, 0)

(no "Exon" information available for 2WKB)

(-) 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:107
 aligned with Q4YQW0_PLABA | Q4YQW0 from UniProtKB/TrEMBL  Length:116

    Alignment length:116
                                                                                                                                            116 
                                    11        21        31        41        51        61        71        81        91       101       111    | 
         Q4YQW0_PLABA     2 PCCELITNISIPDDKAQNTLSEIEDAISNILGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSLLADKITKILSNHLSVKPRRVYIEFRDCSAQNFAFSGSLFG-   -
               SCOP domains d2wkba_ A: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhh......ee.eee....ee.......eeeeee..-----.hhhhhhhhhhhhhhhhhh.hhh.eeeeee.----.eeee.hhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2wkb A   1 PcCELITNISIPDDKAQNTLSEIEDAISNILGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSI-----SNNSLLADKITKILSNHLSVKPRRVYIEFRD----NFAFSGSLFGG 116
                             |      10        20        30        40        50        60    |    -|       80        90       100|    | 110      
                             |                                                             65    71                           101  106          
                             2-CME                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:112
 aligned with Q4YQW0_PLABA | Q4YQW0 from UniProtKB/TrEMBL  Length:116

    Alignment length:115
                                    11        21        31        41        51        61        71        81        91       101       111     
         Q4YQW0_PLABA     2 PCCELITNISIPDDKAQNTLSEIEDAISNILGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSLLADKITKILSNHLSVKPRRVYIEFRDCSAQNFAFSGSLFG 116
               SCOP domains d2wkbb_ B: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhh......ee.eee....ee.......eeeeee........hhhhhhhhhhhhhhhhhh.hhh.eeeeee..---.eeee.hhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2wkb B   1 PcCELITNISIPDDKAQNTLSEIEDAISNILGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSLLADKITKILSNHLSVKPRRVYIEFRDC---NFAFSGSLFG 115
                             |      10        20        30        40        50        60        70        80        90       100 |   | 110     
                             2-CME                                                                                             102 106         


Chain C from PDB  Type:PROTEIN  Length:116
 aligned with Q4YQW0_PLABA | Q4YQW0 from UniProtKB/TrEMBL  Length:116

    Alignment length:116
                                                                                                                                            116 
                                    11        21        31        41        51        61        71        81        91       101       111    | 
         Q4YQW0_PLABA     2 PCCELITNISIPDDKAQNTLSEIEDAISNILGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSLLADKITKILSNHLSVKPRRVYIEFRDCSAQNFAFSGSLFG-   -
               SCOP domains d2wkbc_ C: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhh......ee.eee....ee.......eeeeee........hhhhhhhhhhhhhhhhhh.hhh.eeeeee.....eeeee.hhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2wkb C   1 PcCELITNISIPDDKAQNTLSEIEDAISNILGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSLLADKITKILSNHLSVKPRRVYIEFRDCSAQNFAFSGSLFGG 116
                             |      10        20        30        40        50        60        70        80        90       100       110      
                             2-CME                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:112
 aligned with Q4YQW0_PLABA | Q4YQW0 from UniProtKB/TrEMBL  Length:116

    Alignment length:116
                                                                                                                                            116 
                                    11        21        31        41        51        61        71        81        91       101       111    | 
         Q4YQW0_PLABA     2 PCCELITNISIPDDKAQNTLSEIEDAISNILGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSLLADKITKILSNHLSVKPRRVYIEFRDCSAQNFAFSGSLFG-   -
               SCOP domains d2wkbd_ D: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhh......ee.eee....ee.......eeeeee.....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee..----.eee.hhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2wkb D   1 PcCELITNISIPDDKAQNTLSEIEDAISNILGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSLLADKITKILSNHLSVKPRRVYIEFRDC----FAFSGSLFGG 116
                             |      10        20        30        40        50        60        70        80        90       100 |    |110      
                             2-CME                                                                                             102  107         


Chain E from PDB  Type:PROTEIN  Length:117
 aligned with Q4YQW0_PLABA | Q4YQW0 from UniProtKB/TrEMBL  Length:116

    Alignment length:117
                                                                                                                                            116  
                                    11        21        31        41        51        61        71        81        91       101       111    |  
         Q4YQW0_PLABA     2 PCCELITNISIPDDKAQNTLSEIEDAISNILGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSLLADKITKILSNHLSVKPRRVYIEFRDCSAQNFAFSGSLFG--   -
               SCOP domains d2wkbe_ E: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhh......ee.eee....ee.......eeeeee........hhhhhhhhhhhhhhhhhh.hhh.eeeeee.......eee.hhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2wkb E   1 PcCELITNISIPDDKAQNTLSEIEDAISNILGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSLLADKITKILSNHLSVKPRRVYIEFRDCSAQNFAFSGSLFGGS 117
                             |      10        20        30        40        50        60        70        80        90       100       110       
                             2-CME                                                                                                               


Chain F from PDB  Type:PROTEIN  Length:116
 aligned with Q4YQW0_PLABA | Q4YQW0 from UniProtKB/TrEMBL  Length:116

    Alignment length:116
                                                                                                                                            116 
                                    11        21        31        41        51        61        71        81        91       101       111    | 
         Q4YQW0_PLABA     2 PCCELITNISIPDDKAQNTLSEIEDAISNILGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSLLADKITKILSNHLSVKPRRVYIEFRDCSAQNFAFSGSLFG-   -
               SCOP domains d2wkbf_ F: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) MIF-2wkbF01 F:1-115                                                                                                - Pfam domains (1)
           Pfam domains (2) MIF-2wkbF02 F:1-115                                                                                                - Pfam domains (2)
           Pfam domains (3) MIF-2wkbF03 F:1-115                                                                                                - Pfam domains (3)
           Pfam domains (4) MIF-2wkbF04 F:1-115                                                                                                - Pfam domains (4)
           Pfam domains (5) MIF-2wkbF05 F:1-115                                                                                                - Pfam domains (5)
           Pfam domains (6) MIF-2wkbF06 F:1-115                                                                                                - Pfam domains (6)
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhh......ee.eee....ee.......eeeeee........hhhhhhhhhhhhhhhhhh.hhh.eeeeee.hhh.eeeee.hhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2wkb F   1 PcCELITNISIPDDKAQNTLSEIEDAISNILGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSLLADKITKILSNHLSVKPRRVYIEFRDCSAQNFAFSGSLFGG 116
                             |      10        20        30        40        50        60        70        80        90       100       110      
                             2-CME
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (1, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WKB)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: MIF (36)
(-)
Family: MIF (22)
(-)
Plasmodium berghei (strain Anka) (1)
1aMIF-2wkbF01F:1-115
1bMIF-2wkbF02F:1-115
1cMIF-2wkbF03F:1-115
1dMIF-2wkbF04F:1-115
1eMIF-2wkbF05F:1-115
1fMIF-2wkbF06F:1-115

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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