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

(-) Description

Title :  SP PROTEIN LIGAND 1
 
Authors :  K. L. Longenecker, G. F. Stamper, P. J. Hajduk, E. H. Fry, C. G. Jakob, J. E R. Edalji, D. M. Bartley, K. A. Walter, L. R. Solomon
Date :  08 Aug 05  (Deposition) - 24 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Longenecker, G. F. Stamper, P. J. Hajduk, E. H. Fry, C. G. Jakob, J. E. Harlan, R. Edalji, D. M. Bartley, K. A. Walter, L. R. Solomon, T. F. Holzman, Y. G. Gu, C. G. Lerner, B. A. Beutel, V. S. Stoll
Structure Of Murf From Streptococcus Pneumoniae Co-Crystallized With A Small Molecule Inhibitor Exhibits Interdomain Closure
Protein Sci. V. 14 3039 2005
PubMed-ID: 16322581  |  Reference-DOI: 10.1110/PS.051604805

(-) Compounds

Molecule 1 - UDP-N-ACETYLMURAMOYLALANINE-D-GLUTAMYL-LYSINE-D-ALANYL-D- ALANINE LIGASE, MURF PROTEIN
    Chains: A
    EC Number: 6.3.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MURF
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: R6
    Synonym: SP PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
11LG1Ligand/Ion2,4-DICHLORO-N-(3-CYANO-4,5,6,7-TETRAHYDRO-BENZOTHIOPHEN-2YL)-5-(MORPHOLINE-4-SULFONYL)-BENZAMIDE
2GOL1Ligand/IonGLYCEROL
3MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:31 , ASP A:32 , ARG A:34 , ALA A:48 , ARG A:49 , PHE A:54 , ASN A:134 , TYR A:135 , ASN A:137 , GLY A:140 , ASN A:326 , ASN A:328 , PRO A:329 , THR A:330 , ALA A:331 , LEU A:334 , LEU A:360 , LEU A:367 , GOL A:501BINDING SITE FOR RESIDUE 1LG A 1000
2AC2SOFTWAREPHE A:31 , ASP A:32 , SER A:33 , PHE A:42 , ARG A:49 , GLY A:51 , 1LG A:1000 , HOH A:1001BINDING SITE FOR RESIDUE GOL A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AM1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AM1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AM1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AM1)

(-) Exons   (0, 0)

(no "Exon" information available for 2AM1)

(-) 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:454
 aligned with Q8DNV6_STRR6 | Q8DNV6 from UniProtKB/TrEMBL  Length:457

    Alignment length:454
                                    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       350       360       370       380       390       400       410       420       430       440       450    
         Q8DNV6_STRR6     1 MKLTIHEIAQVVGAKNDISIFEDTQLEKAEFDSRLIGTGDLFVPLKGARDGHDFIETAFENGAAVTLSEKEVSNHPYILVDDVLTAFQSLASYYLEKTTVDVFAVTGSNGKTTTKDMLAHLLSTRYKTYKTQGNYNNEIGLPYTVLHMPEGTEKLVLEMGQDHLGDIHLLSELARPKTAIVTLVGEAHLAFFKDRSEIAKGKMQIADGMASGSLLLAPADPIVEDYLPIDKKVVRFGQGAELEITDLVERKDSLTFKANFLEQALDLPVTGKYNATNAMIASYVALQEGVSEEQIRLAFQHLELTRNRTEWKKAANGADILSDVYNANPTAMKLILETFSAIPANEGGKKIAVLADMKELGDQSVQLHNQMILSLSPDVLDIVIFYGEDIAQLAQLASQMFPIGHVYYFKKTEDQDQFEDLVKQVKESLGAHDQILLKGSNSMNLAKLVESLEN 454
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh...............ee.hhhhh....ee.......hhhhhhhhhhhh...eeee........eee..hhhhhhhhhhhhhhhhhh.eeeeee......hhhhhhhhhhh....eee........hhhhhhhhh......eeeee......hhhhhhhhhhh..eeee............hhhhhhhhhhhhhh......eeeee.hhhhhhhh....eeeee.......eeeeee....eeeee......eee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh........ee......eeeee....hhhhhhhhhhhhh........eeeeeee.......hhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhh....eeeee......hhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2am1 A   1 mKLTIHEIAQVVGAKNDISIFEDTQLEKAEFDSRLIGTGDLFVPLKGARDGHDFIETAFENGAAVTLSEKEVSNHPYILVDDVLTAFQSLASYYLEKTTVDVFAVTGSNGKTTTKDmLAHLLSTRYKTYKTQGNYNNEIGLPYTVLHmPEGTEKLVLEmGQDHLGDIHLLSELARPKTAIVTLVGEAHLAFFKDRSEIAKGKmQIADGmASGSLLLAPADPIVEDYLPIDKKVVRFGQGAELEITDLVERKDSLTFKANFLEQALDLPVTGKYNATNAmIASYVALQEGVSEEQIRLAFQHLELTRNRTEWKKAANGADILSDVYNANPTAmKLILETFSAIPANEGGKKIAVLADmKELGDQSVQLHNQmILSLSPDVLDIVIFYGEDIAQLAQLASQmFPIGHVYYFKKTEDQDQFEDLVKQVKESLGAHDQILLKGSNSmNLAKLVESLEN 454
                            |       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       350      |360       370|      380       390       400       410       420       430       440  |    450    
                            |                                                                                                                 117-MSE                        148-MSE    159-MSE                                     203-MSE |                                                                   279-MSE                                              332-MSE                  357-MSE       371-MSE                      400-MSE                                    443-MSE       
                            1-MSE                                                                                                                                                                                                         209-MSE
   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 2AM1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2AM1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AM1)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8DNV6_STRR6 | Q8DNV6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0047480    UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity    Catalysis of the reaction: UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine + ATP + D-alanyl-D-alanine = phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine + ADP.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    1LG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2am1)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  2am1
    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
  Q8DNV6_STRR6 | Q8DNV6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  6.3.2.10
    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
  Q8DNV6_STRR6 | Q8DNV6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8DNV6_STRR6 | Q8DNV6: 2am2 3zm5 3zm6

(-) Related Entries Specified in the PDB File

2am2 CRYSTAL STRUCTURE OF SP PROTEIN LIGAND 2