Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM FAMILY 3 GLYCOSIDE HYDROLASE (NAGZ) COVALENTLY BOUND TO 5-FLUORO-GLCNAC.
 
Authors :  J. P. Bacik, B. L. Mark
Date :  30 Aug 12  (Deposition) - 19 Dec 12  (Release) - 19 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tim-Barrel, Hydrolase, 5-F-Glcnac, Hydrolase-Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Bacik, G. E. Whitworth, K. A. Stubbs, D. J. Vocadlo, B. L. Mark
Active Site Plasticity Within The Glycoside Hydrolase Nagz Underlies A Dynamic Mechanism Of Substrate Distortion.
Chem. Biol. V. 19 1471 2012
PubMed-ID: 23177201  |  Reference-DOI: 10.1016/J.CHEMBIOL.2012.09.016

(-) Compounds

Molecule 1 - BETA-HEXOSAMINIDASE
    Chains: A, B
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NAGZ, STM1209
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2 / SGSC1412 / ATCC 700720
    Synonym: BETA-N-ACETYLHEXOSAMINIDASE, N-ACETYL-BETA-GLUCOSAMINIDASE

 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, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
10XY2Ligand/IonN-[(2S,3R,4R,5S,6S)-6-FLUORO-2,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-3-YL]ACETAMIDE
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
10XY1Ligand/IonN-[(2S,3R,4R,5S,6S)-6-FLUORO-2,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-3-YL]ACETAMIDE
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10XY1Ligand/IonN-[(2S,3R,4R,5S,6S)-6-FLUORO-2,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-3-YL]ACETAMIDE
2MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:30 , PHE A:32 , ASP A:62 , ARG A:133 , LYS A:163 , HIS A:164 , MET A:210 , ASP A:248 , LEU A:277 , HOH A:779BINDING SITE FOR RESIDUE 0XY A 401
2AC2SOFTWAREARG A:311 , ARG A:312 , MET A:315 , HOH A:559 , HOH A:916 , SER B:310 , ARG B:312 , HOH B:679 , HOH B:680 , HOH B:913BINDING SITE FOR RESIDUE MES A 402
3AC3SOFTWAREILE B:30 , PHE B:32 , ASP B:62 , ARG B:133 , LYS B:163 , HIS B:164 , MET B:210 , ASP B:248 , LEU B:277 , HOH B:753 , HOH B:833 , HOH B:846BINDING SITE FOR RESIDUE 0XY B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ala A:118 -Pro A:119
2Lys A:163 -His A:164
3Phe A:165 -Pro A:166
4Ala B:118 -Pro B:119
5Lys B:163 -His B:164
6Phe B:165 -Pro B:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GVH)

(-) 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:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4gvha_ A: automated matches                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.......hhhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhhhhhh....eeee.eee..ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.............hhhhh...hhhhhhhhhhhhhhhhhhhh...eeeee...................hhhhhhhhhhhhhhhhhhh....eeee...........hhhhhhhhhh...........eeee.hhhhh.hhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gvh A   1 MGPVMLNVEGCELDAEEREILAHPLVGGLILFTRNYHDPEQLRELVRQIRAASRNHLVVAVDQEGGRVQRFREGFTRLPAAQSFFALHGLEEGGRLAQEAGWLMASEMIAMDIDISFAPVLDVGHISAAIGERSYHADPAKALAMATRFIDGMHDAGMKTTGKHFPGHGAVTADSHKETPCDPRPETDIRGKDMSVFRTLISENKLDAIMPAHVIYRAIDPRPASGSPYWLKTVLRQELGFDGVIFSDDLSMEGAAIMGSYAERAQASLDAGCDMILVCNNRKGAVSVLDNLSPIKAERVTRLYHKGSFSRRELMDSARWKTASAQLNQLHERWQEEKAGH 341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 


Chain B from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4gvhb_ B: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.......hhhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhhhhhh....eeee.eee..ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.............hhhhh...hhhhhhhhhhhhhhhhhhhh...eeeee..............hhhhhhhhhhhhhhhhhhh....eeee...........hhhhhhhhhh...........eeee.....hhhhhhhhhhhh..eeee..hhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gvh B   1 MGPVMLNVEGCELDAEEREILAHPLVGGLILFTRNYHDPEQLRELVRQIRAASRNHLVVAVDQEGGRVQRFREGFTRLPAAQSFFALHGLEEGGRLAQEAGWLMASEMIAMDIDISFAPVLDVGHISAAIGERSYHADPAKALAMATRFIDGMHDAGMKTTGKHFPGHGAVTETPCDPRPETDIRGKDMSVFRTLISENKLDAIMPAHVIYRAIDPRPASGSPYWLKTVLRQELGFDGVIFSDDLSSYAERAQASLDAGCDMILVCNNRKGAVSVLDNLSPIKAERVTRLYHKGSFSRRELMDSARWKTASAQLNQLHERWQEEKAGH 341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 ||    185       195       205       215       225       235       245     ||263       273       283       293       303       313       323       333        
                                                                                                                                                                                                     172|                                                                      251|                                                                                 
                                                                                                                                                                                                      178                                                                       260
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    0XY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:118 - Pro A:119   [ RasMol ]  
    Ala B:118 - Pro B:119   [ RasMol ]  
    Lys A:163 - His A:164   [ RasMol ]  
    Lys B:163 - His B:164   [ RasMol ]  
    Phe A:165 - Pro A:166   [ RasMol ]  
    Phe B:165 - Pro B:166   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4gvh
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NAGZ_SALTY | Q8ZQ06
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.52
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  NAGZ_SALTY | Q8ZQ06
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NAGZ_SALTY | Q8ZQ06: 4gvf 4gvg 4gvi 4hzm

(-) Related Entries Specified in the PDB File

4gvf 4gvg 4gvi