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

(-) Description

Title :  CRYSTAL STRUCTURE OF APO D-ALANINE:D-ALANINE LIGASE (DDL) FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  J. B. Bruning, A. C. Murillo, O. Chacon, R. G. Barletta, J. C. Sacchettin Structural Genomics Consortium (Tbsgc)
Date :  23 Feb 10  (Deposition) - 09 Mar 10  (Release) - 05 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  D-Alanine--D-Alanine Ligase, Ddl, D-Alanyl--D-Alanine Ligase, Rv2981C, D-Alanine, Structural Genomics, Tb Structural Genomics Consortium, Tbsgc, Atp-Binding, Cell Shape, Cell Wall Biogenesis, Degradation, Ligase, Magnesium, Manganese, Metal-Binding, Nucleotide-Binding, Peptidoglycan Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bruning, A. C. Murillo, O. Chacon, R. G. Barletta, J. C. Sacchettini
Structure Of The Mycobacterium Tuberculosis D-Alanine:D-Alanine Ligase, A Target Of The Antituberculosi Drug D-Cycloserine.
Antimicrob. Agents Chemother. V. 55 291 2011
PubMed-ID: 20956591  |  Reference-DOI: 10.1128/AAC.00558-10

(-) Compounds

Molecule 1 - D-ALANINE--D-ALANINE LIGASE
    Chains: A, B
    EC Number: 6.3.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP16
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DDL, DDLA, MT3059, MTCY349.06, RV2981C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: D-ALANYLALANINE SYNTHETASE, D-ALA-D-ALA LIGASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NO32Ligand/IonNITRATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:316 , PRO A:335 , GLY A:336 , SER A:341 , MET A:342 , TYR A:343BINDING SITE FOR RESIDUE NO3 A 374
2AC2SOFTWAREARG B:316 , PRO B:335 , GLY B:336 , MET B:342 , TYR B:343BINDING SITE FOR RESIDUE NO3 B 374

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LWB)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Pro A:174 -Pro A:175
2Leu A:189 -Pro A:190
3Val A:286 -Pro A:287
4Leu B:107 -Glu B:108
5Pro B:174 -Pro B:175
6Leu B:189 -Pro B:190
7Val B:286 -Pro B:287
8Gly B:369 -Val B:370

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LWB)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DALA_DALA_LIGASE_1PS00843 D-alanine--D-alanine ligase signature 1.DDL_MYCTO118-129
 		  2A:118-129
B:118-129
DDL_MYCTU118-129
 		  2A:118-129
B:118-129
2DALA_DALA_LIGASE_2PS00844 D-alanine--D-alanine ligase signature 2.DDL_MYCTO309-336
 		  2A:309-336
B:309-336
DDL_MYCTU309-336
 		  2A:309-336
B:309-336

(-) Exons   (0, 0)

(no "Exon" information available for 3LWB)

(-) 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:323
 aligned with DDL_MYCTO | P9WP30 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:362
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366  
            DDL_MYCTO     7 RDRRVRVAVVFGGRSNEHAISCVSAGSILRNLDSRRFDVIAVGITPAGSWVLTDANPDALTITNRELPQVKSGSGTELALPADPRRGGQLVSLPPGAGEVLESVDVVFPVLHGPYGEDGTIQGLLELAGVPYVGAGVLASAVGMDKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERLGLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARRHDPKVIVEAAISGRELECGVLEMPDGTLEASTLGEIRVAGVRGREDSFYDFATKYLDDAAELDVPAKVDDQVAEAIRQLAIRAFAAIDCRGLARVDFFLTDDGPVINEINTMPGFTTISMYPRMWAASGVDYPTLLATMIETALAR 368
               SCOP domains d3lwba1 A:7-1     50 automated matches                                                                                                          d3lwba2 A:151-368 automated matches                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.-----hhhhhhhhhhhhhh....eeeeeeee.....eeee...----------------------------------.....hhhhhhhh..eeee..ee..ee.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......eeee.......hhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhhh....eeeee..eeeeeeeeeee.....eee...eeee.......ee...hhhhhhh....eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          -------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lwb A   7 RDRRVRVAVVFGG-----AISCVSAGSILRNLDSRRFDVIAVGITPAGSWVLTDAN----------------------------------VSLPPGAGEVLESVDVVFPVLHGPYGEDGTIQGLLELAGVPYVGAGVLASAVGMDKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERLGLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARRHDPKVIVEAAISGRELECGVLEMPDGTLEASTLGEIRVAGVRGREDSFYDFATKYLDDAAELDVPAKVDDQVAEAIRQLAIRAFAAIDCRGLARVDFFLTDDGPVINEINTMPGFTTISMYPRMWAASGVDYPTLLATMIETTLAR 368
                                    16  |     26        36        46        56     |   -         -         -         -|      106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366  
                                       19    25                                   62                                 97                                                                                                                                                                                                                                                                               


Chain A from PDB  Type:PROTEIN  Length:323
 aligned with DDL_MYCTU | P9WP31 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:362
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366  
            DDL_MYCTU     7 RDRRVRVAVVFGGRSNEHAISCVSAGSILRNLDSRRFDVIAVGITPAGSWVLTDANPDALTITNRELPQVKSGSGTELALPADPRRGGQLVSLPPGAGEVLESVDVVFPVLHGPYGEDGTIQGLLELAGVPYVGAGVLASAVGMDKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERLGLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARRHDPKVIVEAAISGRELECGVLEMPDGTLEASTLGEIRVAGVRGREDSFYDFATKYLDDAAELDVPAKVDDQVAEAIRQLAIRAFAAIDCRGLARVDFFLTDDGPVINEINTMPGFTTISMYPRMWAASGVDYPTLLATMIETTLAR 368
               SCOP domains d3lwba1 A:7-1     50 automated matches                                                                                                          d3lwba2 A:151-368 automated matches                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.-----hhhhhhhhhhhhhh....eeeeeeee.....eeee...----------------------------------.....hhhhhhhh..eeee..ee..ee.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......eeee.......hhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhhh....eeeee..eeeeeeeeeee.....eee...eeee.......ee...hhhhhhh....eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          -------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lwb A   7 RDRRVRVAVVFGG-----AISCVSAGSILRNLDSRRFDVIAVGITPAGSWVLTDAN----------------------------------VSLPPGAGEVLESVDVVFPVLHGPYGEDGTIQGLLELAGVPYVGAGVLASAVGMDKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERLGLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARRHDPKVIVEAAISGRELECGVLEMPDGTLEASTLGEIRVAGVRGREDSFYDFATKYLDDAAELDVPAKVDDQVAEAIRQLAIRAFAAIDCRGLARVDFFLTDDGPVINEINTMPGFTTISMYPRMWAASGVDYPTLLATMIETTLAR 368
                                    16  |     26        36        46        56     |   -         -         -         -|      106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366  
                                       19    25                                   62                                 97                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:298
 aligned with DDL_MYCTO | P9WP30 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:364
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369    
            DDL_MYCTO    10 RVRVAVVFGGRSNEHAISCVSAGSILRNLDSRRFDVIAVGITPAGSWVLTDANPDALTITNRELPQVKSGSGTELALPADPRRGGQLVSLPPGAGEVLESVDVVFPVLHGPYGEDGTIQGLLELAGVPYVGAGVLASAVGMDKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERLGLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARRHDPKVIVEAAISGRELECGVLEMPDGTLEASTLGEIRVAGVRGREDSFYDFATKYLDDAAELDVPAKVDDQVAEAIRQLAIRAFAAIDCRGLARVDFFLTDDGPVINEINTMPGFTTISMYPRMWAASGVDYPTLLATMIETALARGVGLH 373
               SCOP domains d3lwbb1       B:10-150 automated matches                                                                                                     d3lwbb2 B:151-373 automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Dala_Da      la_lig_N-3lwbB03 B:11-141                                                                                             ----------------Dala_Dala_lig_C-3lwbB01 B:158-363                                                                                                                                                                             ---------- Pfam domains (1)
           Pfam domains (2) -Dala_Da      la_lig_N-3lwbB04 B:11-141                                                                                             ----------------Dala_Dala_lig_C-3lwbB02 B:158-363                                                                                                                                                                             ---------- Pfam domains (2)
         Sec.struct. author .eeeeee.------.hhhhhhhhhhhhhh....eeeeee....-----------------------------------------------------......eeee...-------hhhhhhhh........hhhhhhhhhhhhhhhhhhhhh......eeee.......hhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhhh....eeeee..eeeeeeeeeee.....eee...eeee.......ee...hhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee........hhhhhhhhh...hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lwb B  10 RVRVAVVF------HAISCVSAGSILRNLDSRRFDVIAVGITP-----------------------------------------------------VLESVDVVFPVLH-------TIQGLLELAGVPYVGAGVLASAVGMDKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERLGLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARRHDPKVIVEAAISGRELECGVLEMPDGTLEASTLGEIRVAGVRGREDSFYDFATKYLDDAAELDVPAKVDDQVAEAIRQLAIRAFAAIDCRGLARVDFFLTDDGPVINEINTMPGFTTISMYPRMWAASGVDYPTLLATMIETTLARGVGLH 373
                                   | -    |   29        39        49  |      -         -         -         -         -      |109        |-      |129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369    
                                  17     24                          52                                                   106         118     126                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:298
 aligned with DDL_MYCTU | P9WP31 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:364
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369    
            DDL_MYCTU    10 RVRVAVVFGGRSNEHAISCVSAGSILRNLDSRRFDVIAVGITPAGSWVLTDANPDALTITNRELPQVKSGSGTELALPADPRRGGQLVSLPPGAGEVLESVDVVFPVLHGPYGEDGTIQGLLELAGVPYVGAGVLASAVGMDKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERLGLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARRHDPKVIVEAAISGRELECGVLEMPDGTLEASTLGEIRVAGVRGREDSFYDFATKYLDDAAELDVPAKVDDQVAEAIRQLAIRAFAAIDCRGLARVDFFLTDDGPVINEINTMPGFTTISMYPRMWAASGVDYPTLLATMIETTLARGVGLH 373
               SCOP domains d3lwbb1       B:10-150 automated matches                                                                                                     d3lwbb2 B:151-373 automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Dala_Da      la_lig_N-3lwbB03 B:11-141                                                                                             ----------------Dala_Dala_lig_C-3lwbB01 B:158-363                                                                                                                                                                             ---------- Pfam domains (1)
           Pfam domains (2) -Dala_Da      la_lig_N-3lwbB04 B:11-141                                                                                             ----------------Dala_Dala_lig_C-3lwbB02 B:158-363                                                                                                                                                                             ---------- Pfam domains (2)
         Sec.struct. author .eeeeee.------.hhhhhhhhhhhhhh....eeeeee....-----------------------------------------------------......eeee...-------hhhhhhhh........hhhhhhhhhhhhhhhhhhhhh......eeee.......hhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhhh....eeeee..eeeeeeeeeee.....eee...eeee.......ee...hhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee........hhhhhhhhh...hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lwb B  10 RVRVAVVF------HAISCVSAGSILRNLDSRRFDVIAVGITP-----------------------------------------------------VLESVDVVFPVLH-------TIQGLLELAGVPYVGAGVLASAVGMDKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERLGLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARRHDPKVIVEAAISGRELECGVLEMPDGTLEASTLGEIRVAGVRGREDSFYDFATKYLDDAAELDVPAKVDDQVAEAIRQLAIRAFAAIDCRGLARVDFFLTDDGPVINEINTMPGFTTISMYPRMWAASGVDYPTLLATMIETTLARGVGLH 373
                                   | -    |   29        39        49  |      -         -         -         -         -      |109        |-      |129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369    
                                  17     24                          52                                                   106         118     126
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LWB)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: ATP-grasp (83)
(-)
Clan: no clan defined [family: Dala_Dala_lig_N] (12)

(-) Gene Ontology  (15, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DDL_MYCTU | P9WP31)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008716    D-alanine-D-alanine ligase activity    Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H(+) + phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    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:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B   (DDL_MYCTO | P9WP30)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008716    D-alanine-D-alanine ligase activity    Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H(+) + phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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
    NO3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly B:369 - Val B:370   [ RasMol ]  
    Leu A:189 - Pro A:190   [ RasMol ]  
    Leu B:107 - Glu B:108   [ RasMol ]  
    Leu B:189 - Pro B:190   [ RasMol ]  
    Pro A:174 - Pro A:175   [ RasMol ]  
    Pro B:174 - Pro B:175   [ RasMol ]  
    Val A:286 - Pro A:287   [ RasMol ]  
    Val B:286 - Pro B:287   [ RasMol ]  
 

(-) 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
  3lwb
    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
  DDL_MYCTO | P9WP30
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  DDL_MYCTU | P9WP31
    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)
  6.3.2.4
    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
  DDL_MYCTO | P9WP30
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  DDL_MYCTU | P9WP31
    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 3LWB)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3LWB)