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(-) Description

Title :  STRUCTURE OF APOMIF
 
Authors :  Y. -F. Zhou, X. -D. Su, D. Shao, H. Wang
Date :  17 Feb 09  (Deposition) - 29 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Macrophage Migration Inhibitory Factor, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Shao, X. Zhong, Y. -F. Zhou, Z. Han, Y. Lin, Z. Wang, L. Bu, L. Zhang, X. -D. Su, H. Wang
Structural And Functional Comparison Of Mif Ortholog From Plasmodium Yoelii With Mif From Its Rodent Host
Mol. Immunol. V. 47 726 2010
PubMed-ID: 20004020  |  Reference-DOI: 10.1016/J.MOLIMM.2009.10.037

(-) Compounds

Molecule 1 - MACROPHAGE MIGRATION INHIBITORY FACTOR-LIKE PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MIF
    Organism Scientific: PLASMODIUM YOELII YOELII
    Organism Taxid: 73239

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2SO42Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:92 , ARG A:94 , LYS D:83BINDING SITE FOR RESIDUE SO4 A 119
02AC2SOFTWARELYS B:16 , HIS B:88 , HOH B:146 , HOH B:983 , ARG E:94 , ACY F:1 , HOH F:157 , HOH F:314BINDING SITE FOR RESIDUE SO4 B 1
03AC3SOFTWAREARG B:94 , HOH B:493 , HOH B:976 , LYS E:16 , ASN E:19 , HOH E:127 , HOH E:158 , HOH E:258BINDING SITE FOR RESIDUE SO4 B 119
04AC4SOFTWARELYS C:92 , ARG C:94 , PRO D:13 , HOH D:450BINDING SITE FOR RESIDUE SO4 C 119
05AC5SOFTWAREHOH B:493 , ALA C:37 , TYR C:38 , PHE C:110 , HOH C:127 , HOH C:484BINDING SITE FOR RESIDUE ACY C 1
06AC6SOFTWAREASN C:70 , ASN C:73 , HOH C:151 , HOH C:551 , HOH C:676 , TYR E:45BINDING SITE FOR RESIDUE ACY C 120
07AC7SOFTWAREPHE B:115 , GLU D:56 , LYS D:92 , ARG D:94 , ARG D:95 , HOH D:166 , HOH D:1024BINDING SITE FOR RESIDUE SO4 D 119
08AC8SOFTWARETYR D:97 , PRO E:2 , CYS E:3 , THR E:64 , ILE E:66 , PHE E:108 , HOH E:408BINDING SITE FOR RESIDUE ACY E 1
09AC9SOFTWAREPRO A:13 , LYS F:92 , ARG F:94BINDING SITE FOR RESIDUE SO4 F 119
10BC1SOFTWARESO4 B:1 , ALA F:37 , TYR F:38 , PHE F:110 , HOH F:153 , HOH F:314BINDING SITE FOR RESIDUE ACY F 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GAD)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:115 -Gly A:116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GAD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GAD)

(-) Exons   (0, 0)

(no "Exon" information available for 3GAD)

(-) 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:115
 aligned with Q1HEA2_PLAYO | Q1HEA2 from UniProtKB/TrEMBL  Length:116

    Alignment length:115
                                    11        21        31        41        51        61        71        81        91       101       111     
         Q1HEA2_PLAYO     2 PCCELITNISIPDDKAQNALSEIEDAISNVLGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSSLADKITKILSNHLGVKPRRVYIEFRDCSAQNFAFSGSLFG 116
               SCOP domains d3gada_ A: Microphage migration inhibition factor (MIF)                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhh.hhhh.eeeeee....ee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3gad A   2 PCCELITNISIPDDKAQNALSEIEDAISNVLGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSSLADKITKILSNHLGVKPRRVYIEFRDCSAQNFAFSGSLFG 116
                                    11        21        31        41        51        61        71        81        91       101       111     


Chain B from PDB  Type:PROTEIN  Length:115
 aligned with Q1HEA2_PLAYO | Q1HEA2 from UniProtKB/TrEMBL  Length:116

    Alignment length:115
                                    11        21        31        41        51        61        71        81        91       101       111     
         Q1HEA2_PLAYO     2 PCCELITNISIPDDKAQNALSEIEDAISNVLGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSSLADKITKILSNHLGVKPRRVYIEFRDCSAQNFAFSGSLFG 116
               SCOP domains d3gadb_ B: Microphage migration inhibition factor (MIF)                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhh.hhhh.eeeeee....ee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3gad B   2 PCCELITNISIPDDKAQNALSEIEDAISNVLGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSSLADKITKILSNHLGVKPRRVYIEFRDCSAQNFAFSGSLFG 116
                                    11        21        31        41        51        61        71        81        91       101       111     


Chain C from PDB  Type:PROTEIN  Length:117
 aligned with Q1HEA2_PLAYO | Q1HEA2 from UniProtKB/TrEMBL  Length:116

    Alignment length:117
                                                                                                                                            116  
                                    11        21        31        41        51        61        71        81        91       101       111    |  
         Q1HEA2_PLAYO     2 PCCELITNISIPDDKAQNALSEIEDAISNVLGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSSLADKITKILSNHLGVKPRRVYIEFRDCSAQNFAFSGSLFG--   -
               SCOP domains d3gadc_ C: Microphage migration inhibition factor (MIF)                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhh.hhhh.eeeeee....ee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eee..ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3gad C   2 PCCELITNISIPDDKAQNALSEIEDAISNVLGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSSLADKITKILSNHLGVKPRRVYIEFRDCSAQNFAFSGSLFGLE 118
                                    11        21        31        41        51        61        71        81        91       101       111       


Chain D from PDB  Type:PROTEIN  Length:115
 aligned with Q1HEA2_PLAYO | Q1HEA2 from UniProtKB/TrEMBL  Length:116

    Alignment length:115
                                    11        21        31        41        51        61        71        81        91       101       111     
         Q1HEA2_PLAYO     2 PCCELITNISIPDDKAQNALSEIEDAISNVLGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSSLADKITKILSNHLGVKPRRVYIEFRDCSAQNFAFSGSLFG 116
               SCOP domains d3gadd_ D: Microphage migration inhibition factor (MIF)                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhh.hhhh.eeeeee....ee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3gad D   2 PCCELITNISIPDDKAQNALSEIEDAISNVLGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSSLADKITKILSNHLGVKPRRVYIEFRDCSAQNFAFSGSLFG 116
                                    11        21        31        41        51        61        71        81        91       101       111     


Chain E from PDB  Type:PROTEIN  Length:117
 aligned with Q1HEA2_PLAYO | Q1HEA2 from UniProtKB/TrEMBL  Length:116

    Alignment length:117
                                                                                                                                            116  
                                    11        21        31        41        51        61        71        81        91       101       111    |  
         Q1HEA2_PLAYO     2 PCCELITNISIPDDKAQNALSEIEDAISNVLGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSSLADKITKILSNHLGVKPRRVYIEFRDCSAQNFAFSGSLFG--   -
               SCOP domains d3gade_ E: Microphage migration inhibition factor (MIF)                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhh.hhhh.eeeeee....ee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eee..ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3gad E   2 PCCELITNISIPDDKAQNALSEIEDAISNVLGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSSLADKITKILSNHLGVKPRRVYIEFRDCSAQNFAFSGSLFGLE 118
                                    11        21        31        41        51        61        71        81        91       101       111       


Chain F from PDB  Type:PROTEIN  Length:117
 aligned with Q1HEA2_PLAYO | Q1HEA2 from UniProtKB/TrEMBL  Length:116

    Alignment length:117
                                                                                                                                            116  
                                    11        21        31        41        51        61        71        81        91       101       111    |  
         Q1HEA2_PLAYO     2 PCCELITNISIPDDKAQNALSEIEDAISNVLGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSSLADKITKILSNHLGVKPRRVYIEFRDCSAQNFAFSGSLFG--   -
               SCOP domains d3gadf_ F: Microphage migration inhibition factor (MIF)                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhh.hhhh.eeeeee....ee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eee..ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3gad F   2 PCCELITNISIPDDKAQNALSEIEDAISNVLGKPVAYIMSNYDYQKNLRFSGSNEGYCFVRLTSIGGINRSNNSSLADKITKILSNHLGVKPRRVYIEFRDCSAQNFAFSGSLFGLE 118
                                    11        21        31        41        51        61        71        81        91       101       111
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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  (1, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GAD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GAD)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3GAD)

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        Q1HEA2_PLAYO | Q1HEA2: 3gac

(-) Related Entries Specified in the PDB File

3gac MIF WITH HPP