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 :  STRUCTURE OF ECHA1_1 FROM MYCOBACTERIUM PARATUBERCULOSIS ATCC BAA-968 / K-10
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  25 Mar 11  (Deposition) - 13 Apr 11  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ssgcid, Seattle Structural Genomics Center For Infectious Disease, Enoyl-Coa Hydratase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - ECHA1_1
    Chains: A, B, C
    EC Number: 4.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ECHA1, MAP_2645C
    Organism Scientific: MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS
    Organism Taxid: 1770
    Strain: ATCC BAA-968 / K-10

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1BEZ3Ligand/IonBENZOIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:72 , GLU A:114 , GLU A:134 , ALA A:141 , ALA A:142 , ALA A:143 , MET A:236 , HOH A:279BINDING SITE FOR RESIDUE BEZ A 264
2AC2SOFTWAREILE B:72 , GLU B:114 , GLU B:134 , ALA B:142 , ALA B:143 , HOH B:319BINDING SITE FOR RESIDUE BEZ B 264
3AC3SOFTWAREALA C:67 , GLU C:114 , GLU C:134 , ALA C:141 , ALA C:142 , ALA C:143 , HOH C:323BINDING SITE FOR RESIDUE BEZ C 264

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R9T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3R9T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R9T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R9T)

(-) Exons   (0, 0)

(no "Exon" information available for 3R9T)

(-) 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:260
 aligned with Q73WL5_MYCPA | Q73WL5 from UniProtKB/TrEMBL  Length:263

    Alignment length:260
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
         Q73WL5_MYCPA     4 APGALAERRGNVMVITINRPEARNAINAAVSIGVGDALEEAQHDPEVRAVVLTGAGDKSFCAGADLKAIARRENLYHPDHPEWGFAGYVRHFIDKPTIAAVNGTALGGGTELALASDLVVADERAQFGLPEVKRGLIAAAGGVFRIAEQLPRKVAMRLLLTGEPLSAAAARDWGLINEVVEAGSVLDAALALASAITVNAPLSVQASKRIAYGVDDGVVVGDEPGWDRTMREMRALLKSEDAKEGPRAFAEKREPVWQAR 263
               SCOP domains d3r9ta_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee....eee...hhhhhhh........hhhhhhhhh........eeeee..ee.hhhhhhhhhh.eeeee...ee.hhhhhh......hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhh....eee...hhhhhhhhhhhhhhh.hhhhhhhhhhhhh.ee..ee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r9t A   4 APGALAERRGNVMVITINRPEARNAINAAVSIGVGDALEEAQHDPEVRAVVLTGAGDKSFCAGADLKAIARRENLYHPDHPEWGFAGYVRHFIDKPTIAAVNGTALGGGTELALASDLVVADERAQFGLPEVKRGLIAAAGGVFRIAEQLPRKVAMRLLLTGEPLSAAAARDWGLINEVVEAGSVLDAALALASAITVNAPLSVQASKRIAYGVDDGVVVGDEPGWDRTMREMRALLKSEDAKEGPRAFAEKREPVWQAR 263
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263


Chain B from PDB  Type:PROTEIN  Length:262
 aligned with Q73WL5_MYCPA | Q73WL5 from UniProtKB/TrEMBL  Length:263

    Alignment length:262
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  
         Q73WL5_MYCPA     2 TDAPGALAERRGNVMVITINRPEARNAINAAVSIGVGDALEEAQHDPEVRAVVLTGAGDKSFCAGADLKAIARRENLYHPDHPEWGFAGYVRHFIDKPTIAAVNGTALGGGTELALASDLVVADERAQFGLPEVKRGLIAAAGGVFRIAEQLPRKVAMRLLLTGEPLSAAAARDWGLINEVVEAGSVLDAALALASAITVNAPLSVQASKRIAYGVDDGVVVGDEPGWDRTMREMRALLKSEDAKEGPRAFAEKREPVWQAR 263
               SCOP domains d3r9tb_ B: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee....eee...hhhhhhh........hhhhhhhhh........eeeee..eeehhhhhhhhhh.eeeee...eeehhhhhh......hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhh....eee...hhhhhhhhhhhhhhh.hhhhhhhhhhhhh.ee..ee..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r9t B   2 TDAPGALAERRGNVMVITINRPEARNAINAAVSIGVGDALEEAQHDPEVRAVVLTGAGDKSFCAGADLKAIARRENLYHPDHPEWGFAGYVRHFIDKPTIAAVNGTALGGGTELALASDLVVADERAQFGLPEVKRGLIAAAGGVFRIAEQLPRKVAMRLLLTGEPLSAAAARDWGLINEVVEAGSVLDAALALASAITVNAPLSVQASKRIAYGVDDGVVVGDEPGWDRTMREMRALLKSEDAKEGPRAFAEKREPVWQAR 263
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  


Chain C from PDB  Type:PROTEIN  Length:259
 aligned with Q73WL5_MYCPA | Q73WL5 from UniProtKB/TrEMBL  Length:263

    Alignment length:261
                                    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 
         Q73WL5_MYCPA     3 DAPGALAERRGNVMVITINRPEARNAINAAVSIGVGDALEEAQHDPEVRAVVLTGAGDKSFCAGADLKAIARRENLYHPDHPEWGFAGYVRHFIDKPTIAAVNGTALGGGTELALASDLVVADERAQFGLPEVKRGLIAAAGGVFRIAEQLPRKVAMRLLLTGEPLSAAAARDWGLINEVVEAGSVLDAALALASAITVNAPLSVQASKRIAYGVDDGVVVGDEPGWDRTMREMRALLKSEDAKEGPRAFAEKREPVWQAR 263
               SCOP domains d3r9tc_ C: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----ECH-3r9tC01 C:8-255                                                                                                                                                                                                                                     -------- Pfam domains (1)
           Pfam domains (2) -----ECH-3r9tC02 C:8-255                                                                                                                                                                                                                                     -------- Pfam domains (2)
           Pfam domains (3) -----ECH-3r9tC03 C:8-255                                                                                                                                                                                                                                     -------- Pfam domains (3)
         Sec.struct. author ....eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee....eee...hhhhhhh........hhhhhhhhh........eeeee..eeehhhhhhhhhh.eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhh....eee...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhee..ee..hhhhhhhhhhhhhhhh..hhhhhhhhh--.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r9t C   3 DAPGALAERRGNVMVITINRPEARNAINAAVSIGVGDALEEAQHDPEVRAVVLTGAGDKSFCAGADLKAIARRENLYHPDHPEWGFAGYVRHFIDKPTIAAVNGTALGGGTELALASDLVVADERAQFGLPEVKRGLIAAAGGVFRIAEQLPRKVAMRLLLTGEPLSAAAARDWGLINEVVEAGSVLDAALALASAITVNAPLSVQASKRIAYGVDDGVVVGDEPGWDRTMREMRALLKSEDAKEGPRA--EKREPVWQAR 263
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242        |- |     262 
                                                                                                                                                                                                                                                                                  251  |         
                                                                                                                                                                                                                                                                                     254
   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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R9T)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: ClpP_crotonase (88)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q73WL5_MYCPA | Q73WL5)
molecular function
    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.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 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
    BEZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3r9t)
 

(-) 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
  3r9t
    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
  Q73WL5_MYCPA | Q73WL5
    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)
  4.2.1.17
    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
  Q73WL5_MYCPA | Q73WL5
    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 3R9T)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3R9T)