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(-) Description

Title :  ANCYLOSTOMA CEYLANICUM MIF IN COMPLEX WITH N-(2,3,4,5,6-PENTAFLUORO-BENZYL)-4-SULFAMOYL-BENZAMIDE
 
Authors :  Y. Cho, E. Lolis
Date :  05 Apr 11  (Deposition) - 12 Oct 11  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A (2x),B (2x),C (2x)
Keywords :  Protein-Small Molecule Complex, Isomerase, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Cho, J. J. Vermeire, J. S. Merkel, L. Leng, X. Du, R. Bucala, M. Cappello, E. Lolis
Drug Repositioning And Pharmacophore Identification In The Discovery Of Hookworm Mif Inhibitors.
Chem. Biol. V. 18 1089 2011
PubMed-ID: 21944748  |  Reference-DOI: 10.1016/J.CHEMBIOL.2011.07.011

(-) Compounds

Molecule 1 - MACROPHAGE MIGRATION INHIBITORY FACTOR
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-117
    Organism Scientific: ANCYLOSTOMA CEYLANICUM
    Organism Taxid: 53326

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (2x): A (2x)B (2x)C (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2FUZ3Ligand/Ion2-[(FURAN-2-YLMETHYL)AMINO]BENZOIC ACID
3IMD3Ligand/IonIMIDAZOLE
4ZN7Ligand/IonZINC ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2FUZ3Ligand/Ion2-[(FURAN-2-YLMETHYL)AMINO]BENZOIC ACID
3IMD3Ligand/IonIMIDAZOLE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2FUZ2Ligand/Ion2-[(FURAN-2-YLMETHYL)AMINO]BENZOIC ACID
3IMD4Ligand/IonIMIDAZOLE
4ZN-1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:1 , MET A:2 , LYS A:32 , ARG A:36 , SER A:63 , ILE A:64 , VAL A:106 , PHE A:108 , VAL A:113 , HIS C:49 , ILE C:95BINDING SITE FOR RESIDUE FUZ A 202
02AC2SOFTWAREASP A:70 , ZN A:119 , ACT A:124 , GLY B:44 , ARG B:46 , ASP C:11BINDING SITE FOR RESIDUE IMD A 117
03AC3SOFTWAREGLY A:44 , ARG A:46 , ACT A:123 , ASP B:11 , ZN B:117BINDING SITE FOR RESIDUE IMD A 118
04AC4SOFTWAREASP A:70 , IMD A:117 , ACT A:124 , ASP C:11BINDING SITE FOR RESIDUE ZN A 119
05AC5SOFTWAREASP A:11 , ACT A:122 , HOH A:140 , IMD C:117BINDING SITE FOR RESIDUE ZN A 120
06AC6SOFTWAREGLU A:20 , ASP A:24BINDING SITE FOR RESIDUE ZN A 121
07AC7SOFTWAREASP A:11 , ZN A:120 , ARG C:46 , IMD C:117BINDING SITE FOR RESIDUE ACT A 122
08AC8SOFTWAREARG A:46 , IMD A:118 , ASP B:11 , ZN B:117BINDING SITE FOR RESIDUE ACT A 123
09AC9SOFTWAREASP A:70 , IMD A:117 , ZN A:119 , ARG B:46 , ARG B:53 , ASP C:11BINDING SITE FOR RESIDUE ACT A 124
10BC1SOFTWAREHIS A:49 , ILE A:95 , PRO B:1 , MET B:2 , LYS B:32 , ARG B:36 , ILE B:64 , VAL B:106 , PHE B:108 , VAL B:113BINDING SITE FOR RESIDUE FUZ B 201
11BC2SOFTWAREIMD A:118 , ACT A:123 , HOH A:181 , ASP B:11BINDING SITE FOR RESIDUE ZN B 117
12BC3SOFTWAREGLU B:20 , ASP B:24 , GLU C:20 , ASP C:24BINDING SITE FOR RESIDUE ZN B 118
13BC4SOFTWAREHIS B:49 , ILE B:95 , PRO C:1 , MET C:2 , LYS C:32 , ARG C:36 , ILE C:64 , VAL C:106 , PHE C:108 , VAL C:113BINDING SITE FOR RESIDUE FUZ C 203
14BC5SOFTWAREASP A:11 , ZN A:120 , ACT A:122 , GLY C:44 , ARG C:46BINDING SITE FOR RESIDUE IMD C 117
15BC6SOFTWAREASP C:71 , ACT C:120BINDING SITE FOR RESIDUE ZN C 118
16BC7SOFTWAREALA C:116BINDING SITE FOR RESIDUE ZN C 119
17BC8SOFTWAREMET C:30 , ASN C:31 , ALA C:66 , SER C:68 , ASP C:71 , ARG C:74 , ZN C:118 , HOH C:181 , HOH C:194BINDING SITE FOR RESIDUE ACT C 120

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RF5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RF5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RF5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RF5)

(-) Exons   (0, 0)

(no "Exon" information available for 3RF5)

(-) 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:116
 aligned with A4GRE3_9BILA | A4GRE3 from UniProtKB/TrEMBL  Length:119

    Alignment length:116
                                    11        21        31        41        51        61        71        81        91       101       111      
         A4GRE3_9BILA     2 PMVRVATNLPDKDVPANFEERLTDLLAESMNKPRNRIAIEVLAGQRITHGASRNPVAVIKVESIGALSADDNIRHTQKITQFCQDTLKLPKDKVIITYFDLQPIHVGFNGTTVAAA 117
               SCOP domains d3rf5a_ A: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhh.eeeee...eeee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eee..ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3rf5 A   1 PMVRVATNLPDKDVPANFEERLTDLLAESMNKPRNRIAIEVLAGQRITHGASRNPVAVIKVESIGALSADDNIRHTQKITQFCQDTLKLPKDKVIITYFDLQPIHVGFNGTTVAAA 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with A4GRE3_9BILA | A4GRE3 from UniProtKB/TrEMBL  Length:119

    Alignment length:116
                                    11        21        31        41        51        61        71        81        91       101       111      
         A4GRE3_9BILA     2 PMVRVATNLPDKDVPANFEERLTDLLAESMNKPRNRIAIEVLAGQRITHGASRNPVAVIKVESIGALSADDNIRHTQKITQFCQDTLKLPKDKVIITYFDLQPIHVGFNGTTVAAA 117
               SCOP domains d3rf5b_ B: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhh.eeeee...eeee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.....eeeeeee.hhh.eee..ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3rf5 B   1 PMVRVATNLPDKDVPANFEERLTDLLAESMNKPRNRIAIEVLAGQRITHGASRNPVAVIKVESIGALSADDNIRHTQKITQFCQDTLKLPKDKVIITYFDLQPIHVGFNGTTVAAA 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain C from PDB  Type:PROTEIN  Length:116
 aligned with A4GRE3_9BILA | A4GRE3 from UniProtKB/TrEMBL  Length:119

    Alignment length:116
                                    11        21        31        41        51        61        71        81        91       101       111      
         A4GRE3_9BILA     2 PMVRVATNLPDKDVPANFEERLTDLLAESMNKPRNRIAIEVLAGQRITHGASRNPVAVIKVESIGALSADDNIRHTQKITQFCQDTLKLPKDKVIITYFDLQPIHVGFNGTTVAAA 117
               SCOP domains d3rf5c_ C: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhh..hhhh.eeeee...eeee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.....eeeeeee.hhh.eee..ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3rf5 C   1 PMVRVATNLPDKDVPANFEERLTDLLAESMNKPRNRIAIEVLAGQRITHGASRNPVAVIKVESIGALSADDNIRHTQKITQFCQDTLKLPKDKVIITYFDLQPIHVGFNGTTVAAA 116
                                    10        20        30        40        50        60        70        80        90       100       110
   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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RF5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RF5)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (A4GRE3_9BILA | A4GRE3)
molecular function
    GO:0005126    cytokine receptor binding    Interacting selectively and non-covalently with a cytokine receptor.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/TrEMBL
        A4GRE3_9BILA | A4GRE3: 2os5 3rf4

(-) Related Entries Specified in the PDB File

2os5 ACEMIF APO FORM
3rf4 ACEMIF IN COMPLEX WITH FUROSEMIDE