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(-) Description

Title :  CRYSTAL STRUCTURE OF BURKHOLDERIA CENOCEPACIA FAMILY 3 GLYCOSIDE HYDROLASE (NAGZ) BOUND TO (3S,4R,5R,6S)-3-ACETAMIDO-4,5,6-TRIHYDROXYAZEPANE
 
Authors :  G. Vadlamani, B. L. Mark
Date :  18 Sep 13  (Deposition) - 30 Oct 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tim Barrel, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mondon, S. Hur, G. Vadlamani, P. Rodrigues, P. Tsybina, A. Oliver, B. L. Mark, D. J. Vocadlo, Y. Bleriot
Selective Trihydroxyazepane Nagz Inhibitors Increase Sensitivity Of Pseudomonas Aeruginosa To Beta-Lactams.
Chem. Commun. (Camb. ) V. 49 10983 2013
PubMed-ID: 24136176  |  Reference-DOI: 10.1039/C3CC46646A

(-) Compounds

Molecule 1 - BETA-HEXOSAMINIDASE 1
    Chains: A, B
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BCAL1010, BCAL2860, BCEJ2315_10000, BCEJ2315_27960, NAGZ, NAGZ1, NAGZ2
    Organism Scientific: BURKHOLDERIA CENOCEPACIA
    Organism Taxid: 216591
    Strain: J2315 / LMG 16656
    Synonym: FAMILY 3 GLYCOSIDE HYDROLASE, NAGZ, BETA-HEXOSAMINIDASE 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
12CZ2Ligand/IonN-[(3S,4R,5R,6S)-4,5,6-TRIHYDROXYAZEPAN-3-YL]ACETAMIDE
2GOL3Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
12CZ1Ligand/IonN-[(3S,4R,5R,6S)-4,5,6-TRIHYDROXYAZEPAN-3-YL]ACETAMIDE
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
12CZ1Ligand/IonN-[(3S,4R,5R,6S)-4,5,6-TRIHYDROXYAZEPAN-3-YL]ACETAMIDE
2GOL2Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:65 , ARG A:140 , LYS A:170 , HIS A:171 , SER A:182 , HIS A:183 , ASP A:253 , ASP A:254 , MET A:257 , HOH A:519 , HOH A:749 , HOH A:844BINDING SITE FOR RESIDUE 2CZ A 401
2AC2SOFTWARESER A:18 , ALA A:22 , HOH A:646 , HOH A:823BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREASP B:65 , ARG B:140 , LYS B:170 , HIS B:171 , SER B:182 , HIS B:183 , ASP B:253 , MET B:257 , HOH B:551 , HOH B:631 , HOH B:814BINDING SITE FOR RESIDUE 2CZ B 401
4AC4SOFTWAREALA B:37 , ARG B:70 , VAL B:71 , GLN B:72 , ARG B:73 , ARG B:75 , HOH B:616 , HOH B:753BINDING SITE FOR RESIDUE GOL B 402
5AC5SOFTWAREGLU B:291 , ASN B:295 , HOH B:663 , HOH B:829BINDING SITE FOR RESIDUE GOL B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr A:124 -Pro A:125
2Lys A:170 -His A:171
3Phe A:172 -Pro A:173
4Thr B:124 -Pro B:125
5Lys B:170 -His B:171
6Phe B:172 -Pro B:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MSS)

(-) 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:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.......hhhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhhhhhh...eeee.eee..ee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..............hhhhh...hhhhhhhhhhhhhhhhhhh.....eeee...............ee..hhhhhhhh.hhhhhhhhhhh.eeee...ee......hhhhhhhhhh...........ee......hhhhhhhhhhhhhhhhhhhhh...ee...hhhhhhhhhhhh....hhhhhhhhhh........hhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mss A   3 TTPGPVMLDVVGTTLSRDDARRLAHPNTGGVILFARHFQNRAQLTALTDSIRAVREDILIAVDHEGGRVQRFRTDGFTVLPAMRRLGELWDRDVLLATKVATAVGYILAAELRACGIDMSFTPVLDLDYGHSKVIGDRAFHRDPRVVTLLAKSLNHGLSLAGMANCGKHFPGHGFAEADSHVALPTDDRTLDAILEQDVAPYDWLGLSLAAVIPAHVIYTQVDKRPAGFSRVWLQDILRGKLGFTGAIFSDDLSMEAAREGGTLTQAADAALAAGCDMVLVCNQPDAAEVVLNGLKARASAESVRRIKRMRARGKALKWDKLIAQPEYLQAQALLSSALA 342
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342


Chain B from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.......hhhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhhhhhh...eeee.eee..ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee..............hhhhh...hhhhhhhhhhhhhhhhhhh.....eeee...............ee..hhhhhhhh.hhhhhhhhhhh.eeee...ee......hhhhhhhhhh...........ee......hhhhhhhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhh....hhhhhhhhhh........hhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mss B   3 TTPGPVMLDVVGTTLSRDDARRLAHPNTGGVILFARHFQNRAQLTALTDSIRAVREDILIAVDHEGGRVQRFRTDGFTVLPAMRRLGELWDRDVLLATKVATAVGYILAAELRACGIDMSFTPVLDLDYGHSKVIGDRAFHRDPRVVTLLAKSLNHGLSLAGMANCGKHFPGHGFAEADSHVALPTDDRTLDAILEQDVAPYDWLGLSLAAVIPAHVIYTQVDKRPAGFSRVWLQDILRGKLGFTGAIFSDDLSMEAAREGGTLTQAADAALAAGCDMVLVCNQPDAAEVVLNGLKARASAESVRRIKRMRARGKALKWDKLIAQPEYLQAQALLSSAL 341
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        B4EA43_BURCJ | B4EA43: 4g6c 4gnv

(-) Related Entries Specified in the PDB File

4g6c BURKHOLDERIA CENOCEPACIA FAMILY 3 GLYCOSIDE HYDROLASE (NAGZ) WITHOUT LIGAND
4gnv BURKHOLDERIA CENOCEPACIA FAMILY 3 GLYCOSIDE HYDROLASE (NAGZ) COMPLEXED WITH GLCNAC