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(-) Description

Title :  CRYSTAL STRUCUTRE OF UDP-GALACTOPYRANOSE MUTASE FROM CORYNEBACTERIUM DIPHTHERIAE IN COMPLEX WITH 2-[4-(4-CHLOROPHENYL)-7-(2-THIENYL)-2-THIA-5,6,8,9-TETRAZABICYCLO[4.3.0]NONA-4,7,9-TRIEN-3-YL]ACETIC
 
Authors :  K. Wangkanont, A. Heroux, K. T. Forest, L. L. Kiessling
Date :  31 Dec 14  (Deposition) - 12 Aug 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Udp-Galactopyranose Mutase, Corynebacterium Diphtheriae, Inhibitor, Galactofuranose, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. A. Kincaid, N. London, K. Wangkanont, D. A. Wesener, S. A. Marcus, A. Heroux, L. Nedyalkova, A. M. Talaat, K. T. Forest, B. K. Shoichet, L. L. Kiessling
Virtual Screening For Udp-Galactopyranose Mutase Ligands Identifies A New Class Of Antimycobacterial Agents.
Acs Chem. Biol. V. 10 2209 2015
PubMed-ID: 26214585  |  Reference-DOI: 10.1021/ACSCHEMBIO.5B00370

(-) Compounds

Molecule 1 - UDP-GALACTOPYRANOSE MUTASE
    Chains: A, B
    EC Number: 5.4.99.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL C5X
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 18-404
    Gene: GLF, DIP2203
    Organism Scientific: CORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid: 257309
    Strain: ATCC 700971 / NCTC 13129 / BIOTYPE GRAVIS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
140K2Ligand/Ion[(7S)-6-(4-CHLOROPHENYL)-3-(THIOPHEN-2-YL)-7H-[1,2,4]TRIAZOLO[3,4-B][1,3,4]THIADIAZIN-7-YL]ACETIC ACID
2FDA2Ligand/IonDIHYDROFLAVINE-ADENINE DINUCLEOTIDE
3SO411Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:334 , ARG A:341binding site for residue SO4 A 401
02AC2SOFTWAREGLN A:161 , TRP A:162 , ARG A:288 , SER A:315 , TYR A:326 , PRO A:327 , TYR A:364binding site for residue 40K A 402
03AC3SOFTWAREGLY A:10 , GLY A:12 , LEU A:13 , PHE A:14 , VAL A:33 , GLU A:34 , LYS A:35 , ARG A:36 , GLY A:41 , ASN A:42 , TYR A:58 , ALA A:60 , HIS A:61 , LEU A:62 , THR A:219 , ASP A:220 , TRP A:221 , PHE A:222 , PRO A:242 , TYR A:325 , TYR A:326 , GLY A:357 , ARG A:358 , TYR A:364 , LEU A:365 , ASP A:366 , MET A:367 , ALA A:370 , HOH A:505 , HOH A:507 , HOH A:509 , HOH A:514binding site for residue FDA A 403
04AC4SOFTWAREILE A:129 , ASP A:130 , SER A:131binding site for residue SO4 A 404
05AC5SOFTWAREARG A:119binding site for residue SO4 A 405
06AC6SOFTWARETHR A:81 , GLY A:82 , GLU A:298binding site for residue SO4 A 406
07AC7SOFTWAREPRO A:304 , LYS A:305binding site for residue SO4 A 407
08AC8SOFTWAREARG B:334 , ARG B:341binding site for residue SO4 B 401
09AC9SOFTWAREGLN B:161 , SER B:315 , TYR B:326 , PRO B:327 , TYR B:364binding site for residue 40K B 402
10AD1SOFTWAREVAL B:9 , GLY B:10 , GLY B:12 , LEU B:13 , PHE B:14 , VAL B:33 , GLU B:34 , LYS B:35 , ARG B:36 , GLY B:40 , GLY B:41 , ASN B:42 , TYR B:58 , ALA B:60 , HIS B:61 , LEU B:62 , THR B:219 , TRP B:221 , PHE B:222 , THR B:240 , TYR B:325 , GLY B:357 , ARG B:358 , TYR B:364 , LEU B:365 , ASP B:366 , MET B:367binding site for residue FDA B 403
11AD2SOFTWAREASP B:130 , SER B:131binding site for residue SO4 B 404
12AD3SOFTWAREARG B:119binding site for residue SO4 B 405
13AD4SOFTWAREARG B:36 , SER B:37 , HIS B:38 , TYR B:58binding site for residue SO4 B 406
14AD5SOFTWAREARG B:334 , PHE B:338binding site for residue SO4 B 407
15AD6SOFTWAREGLU B:262 , TYR B:314binding site for residue SO4 B 408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XGK)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XGK)

(-) Sequences/Alignments

Asymmetric/Biological 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:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhhh...eeee......hhhh.eee......eee......eee.hhhhhhhhh............eeee..eeee...hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh......................eee...hhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eee..hhhhhh........eeeeeeeeeee.........eeee........eeee.hhhhhhhh.......eeeeeeeeee........ee..hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xgk A   2 SDFDLIVVGSGLFGLTVAERAASQLGKKVLIVEKRSHLGGNAYSEAEPETGIEIHKYGAHLFHTSNKRVWDYVNQFTAFTGYQHRVFAMHNGTAYQFPMGLGLINQFFGRYYTPDEARELIKEQSAEIDSKDATNLEEKAISLIGRPLYEAFIRDYTAKQWQTDPKELPAGNITRLPVRYNFDNRYFNDTYEGLPVDGYAQWLSNMADHENIEVRLDTDWFEVREDLRAQNPEAPVVYTGPLDRYFDYSEGHLGWRTLDFETEVLNTGDFQGTPVMNYNDAEFPYTRIHEFRHFHPEREDRHPKDKTVIMKEYSRFAEEGDEPYYPINTPSDREMLFKYRELADAETESGKVYFGGRLGTYQYLDMHMAIASALSMFDNKLVDALK 387
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381      


Chain B from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhhhh..eeee...........eee......eee......eee.hhhhhhhhhh..........eeeee..eeee...hhhhhhhhhh...hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.................eee....hhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eee..hhhhhh........eeeeeeeeeee.........eeee........eeee.hhhhhhhh.......eeeeeeeeee........ee..hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhh...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xgk B   2 SDFDLIVVGSGLFGLTVAERAASQLGKKVLIVEKRSHLGGNAYSEAEPETGIEIHKYGAHLFHTSNKRVWDYVNQFTAFTGYQHRVFAMHNGTAYQFPMGLGLINQFFGRYYTPDEARELIKEQSAEIDSKDATNLEEKAISLIGRPLYEAFIRDYTAKQWQTDPKELPAGNITRLPVRYNFDNRYFNDTYEGLPVDGYAQWLSNMADHENIEVRLDTDWFEVREDLRAQNPEAPVVYTGPLDRYFDYSEGHLGWRTLDFETEVLNTGDFQGTPVMNYNDAEFPYTRIHEFRHFHPEREDRHPKDKTVIMKEYSRFAEEGDEPYYPINTPSDREMLFKYRELADAETESGKVYFGGRLGTYQYLDMHMAIASALSMFDNKLVDALK 387
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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