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 :  2.25 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF UDP-N-ACETYLMURAMATE--L-ALANINE LIGASE (MURC) FROM YERSINIA PESTIS CO92 IN COMPLEX WITH AMP
 
Authors :  A. S. Halavaty, G. Minasov, I. Dubrovska, J. Winsor, L. Shuvalova, S. Pe W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date :  05 Nov 12  (Deposition) - 21 Nov 12  (Release) - 21 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Udp-N-Acetylmuramate-L-Alanine Ligase, Murc, Yersinia Pestis Co92, Peptidoglycan Synthesis, Center For Structural Genomics Of Infectious Diseases (Csgid), Niaid, National Institute Of Allergy And Infectious Diseases, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, G. Minasov, I. Dubrovska, J. Winsor, L. Shuvalova, S. Peterson, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
2. 25 Angstrom Resolution Crystal Structure Of Udp-N-Acetylmuramate--L-Alanine Ligase (Murc) From Yersinia Pestis Co92 In Complex With Amp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UDP-N-ACETYLMURAMATE--L-ALANINE LIGASE
    Chains: A, B
    EC Number: 6.3.2.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: MURC, Y3625, YPO0556, YP_3628
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92
    Synonym: UDP-N-ACETYLMURAMOYL-L-ALANINE SYNTHETASE

 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, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2BME2Ligand/IonBETA-MERCAPTOETHANOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2BME1Ligand/IonBETA-MERCAPTOETHANOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2BME1Ligand/IonBETA-MERCAPTOETHANOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:128 , GLY A:129 , LYS A:130 , THR A:131 , THR A:132 , ASN A:194 , HIS A:292 , ASN A:296 , ARG A:327 , ASP A:351 , TYR A:352 , GLY A:353 , GLU A:358 , ALA A:361 , THR A:362 , HOH A:662 , HOH A:683 , HOH A:706BINDING SITE FOR RESIDUE AMP A 501
2AC2SOFTWARECYS A:426 , ARG A:427BINDING SITE FOR RESIDUE BME A 502
3AC3SOFTWAREHIS B:128 , GLY B:129 , LYS B:130 , THR B:131 , THR B:132 , ASN B:194 , HIS B:292 , ASN B:296 , ARG B:327 , ASP B:351 , TYR B:352 , GLY B:353 , GLU B:358 , THR B:362 , HOH B:664 , HOH B:701 , HOH B:703 , HOH B:727BINDING SITE FOR RESIDUE AMP B 501
4AC4SOFTWARECYS B:426 , ARG B:430BINDING SITE FOR RESIDUE BME B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HV4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HV4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HV4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HV4)

(-) Exons   (0, 0)

(no "Exon" information available for 4HV4)

(-) 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:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4hv4a1 A:19-107 automated matches                                                       d4hv4a2 A:108-322 automated matches                                                                                                                                                                                    d4hv4a3 A:323-483 automated matches                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh..eeeee....hhhhhhhhhh..eee...hhhhhh...eeee.......hhhhhhhhhh...eeehhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh....eeeeeeee....eeee.....eeeee..hhhhhhhhh...eeee............hhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhh...eeeee......eeeeeeeee..eeeeeee......eeeee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......eeeeeeehhhhhh...eeeeeee...hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhh......eee....hhhhhhhhhh...eeeeee...hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hv4 A  19 VRHIHFVGIGGAGMGGIAEVLANEGYQISGSDLAPNSVTQHLTALGAQIYFHHRPENVLDASVVVVSTAISADNPEIVAAREARIPVIRRAEMLAELMRYRHGIAVAGTHGKTTTTAMLSSIYAEAGLDPTFVNGGLVKAAGTHARLGSSRYLIAEADESDASFLHLQPMVAIVTNIEADHMDTYQGDFENLKQTFINFLHNLPFYGRAVMCIDDPVVRELLPRVGRHITTYGFSDDADVQIASYRQEGPQGHFTLRRQDKPLIEVTLNAPGRHNALNAAAAVAVATEEGIEDEDILRALVGFQGTGRRFDFLGNFPLAPVNGKEGSAMLVDDYGHHPTEVDATIKAARAGWPDKRIVMLFQPHRYTRTRDLYDDFANVLSQVDVLLMLDVYAAGEPPIPGADSRALCRTIRNRGKLDPILVPDSESAPEMLAQILNGEDLILVQGAGNIGKIARKLAEHKLQPQ 483
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478     


Chain B from PDB  Type:PROTEIN  Length:462
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4hv4b1 B:15-107 automated matches                                                           d4hv4b2 B:108-322 automated matches                                                                                                                                                                             d4hv4b3 B:323-483 automated matches                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.eeeee...hhhhhhhhhhhhhhh.eeeee....hhhhhhhhhh..eee...hhhhhh...eeee.......hhhhhhhhhh...eeehhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh....eee...........ee.....eeeee..hhhhhhhhh...eeee.......hhhhhhhhhhhhh......eeeee..hhhhhhhhhhh..eeeeee......eeeeeeeee..eeeeeeee.....eeeee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......eeeeeeehhhhhh...eeeeeee...hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhh.....eee....hhhhhhhhhh...eeeeee...hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hv4 B  15 EMRRVRHIHFVGIGGAGMGGIAEVLANEGYQISGSDLAPNSVTQHLTALGAQIYFHHRPENVLDASVVVVSTAISADNPEIVAAREARIPVIRRAEMLAELMRYRHGIAVAGTHGKTTTTAMLSSIYAEAGLDPTFVNGGLVKAAGTHARLGSSRYLIAEADESDASFLHLQPMVAIVTNIEADDFENLKQTFINFLHNLPFYGRAVMCIDDPVVRELLPRVGRHITTYGFSDDADVQIASYRQEGPQGHFTLRRQDKPLIEVTLNAPGRHNALNAAAAVAVATEEGIEDEDILRALVGFQGTGRRFDFLGNFPLAPVNGKEGSAMLVDDYGHHPTEVDATIKAARAGWPDKRIVMLFQPHRYTRTRDLYDDFANVLSQVDVLLMLDVYAAGEPPIPGADSRALCRTIRNRGKLDPILVPDSESAPEMLAQILNGEDLILVQGAGNIGKIARKLAEHKLQPQ 483
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194   ||  211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481  
                                                                                                                                                                                                                 198|                                                                                                                                                                                                                                                                                     
                                                                                                                                                                                                                  206
   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  (3, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HV4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HV4)

(-) Gene Ontology  (11, 11)

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
    AMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4hv4)
 
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
  4hv4
    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
  MURC_YERPE | Q8ZIE8
    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)
  6.3.2.8
    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
  MURC_YERPE | Q8ZIE8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4HV4)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4HV4)