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

(-) Description

Title :  THE CRYSTAL STRUCTURE OF MENB (RV0548C) FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH THE COA PORTION OF NAPHTHOYL COA
 
Authors :  J. M. Johnston, V. L. Arcus, E. N. Baker, Tb Structural Genomics Cons (Tbsgc)
Date :  19 Nov 03  (Deposition) - 30 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Crotonase-Like Family, Beta-Beta-Alpha, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Johnston, V. L. Arcus, E. N. Baker
The Crystal Structure Of Menb (Rv0548C) From Mycobacterium Tuberculosis In Complex With The Coa Portion Of Naphthoyl Coa
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MENB
    Chains: A, B, C
    EC Number: 4.1.3.36
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX HTA
    Expression System Strain: BL21 PRI592
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MENB (RV0548C)
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2EP11Ligand/Ion3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONICACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1COA2Ligand/IonCOENZYME A
2EP12Ligand/Ion3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONICACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL B:57 , ARG B:58 , LYS B:95 , SER B:103 , GLY B:105 , ASP B:106 , GLN B:107 , TRP B:157BINDING SITE FOR RESIDUE COA B 1210
2AC2SOFTWAREALA A:201 , ARG A:202 , GLN A:203 , VAL A:204 , GLY A:205 , PHE A:208 , MET A:227 , GLY A:228 , ALA B:201 , ARG B:202 , GLN B:203 , VAL B:204 , GLY B:205 , GLN B:226 , MET B:227 , HOH B:1219 , HOH B:1229 , HOH B:1238 , ALA C:201 , ARG C:202 , GLN C:203 , VAL C:204 , GLY C:205 , PHE C:208 , GLN C:226 , MET C:227 , HOH C:321BINDING SITE FOR RESIDUE EP1 B 1211

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RJN)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:91 -Pro A:92
2Gly B:91 -Pro B:92
3Gly C:91 -Pro C:92

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RJN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RJN)

(-) Exons   (0, 0)

(no "Exon" information available for 1RJN)

(-) 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:259
 aligned with MENB_MYCTO | P9WNP4 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:280
                                    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
           MENB_MYCTO    17 DNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQYASGDTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRLAYMTDEAVEGR 296
               SCOP domains d1rjna_ A: Naphthoate synthase MenB                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1rjnA01 A:17-251 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                                  --------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eee.........eeeeee....eeeeee.hhhhh...hhhhhhhhhhhhhhhhh.....eeeeee..........eee.....---------------------.....hhhhhhhhhhhhh..eeeeee..eeehhhhhhhhhh.eeeee....eee.hhhhhh.......hhhhhhhhhhhhhhhhhhhh.eehhhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rjn A  17 DNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQ---------------------ARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRLAYMTDEAVEGR 296
                                    26        36        46        56        66        76        86        96       106|        -         -  |    136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296
                                                                                                                    107                   129                                                                                                                                                                       


Chain A from PDB  Type:PROTEIN  Length:259
 aligned with MENB_MYCTU | P9WNP5 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:280
                                    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
           MENB_MYCTU    17 DNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQYASGDTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRLAYMTDEAVEGR 296
               SCOP domains d1rjna_ A: Naphthoate synthase MenB                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1rjnA01 A:17-251 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                                  --------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eee.........eeeeee....eeeeee.hhhhh...hhhhhhhhhhhhhhhhh.....eeeeee..........eee.....---------------------.....hhhhhhhhhhhhh..eeeeee..eeehhhhhhhhhh.eeeee....eee.hhhhhh.......hhhhhhhhhhhhhhhhhhhh.eehhhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rjn A  17 DNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQ---------------------ARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRLAYMTDEAVEGR 296
                                    26        36        46        56        66        76        86        96       106|        -         -  |    136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296
                                                                                                                    107                   129                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:275
 aligned with MENB_MYCTO | P9WNP4 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:301
                                    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       273       283       293       303       313 
           MENB_MYCTO    14 ALSDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQYASGDTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRLAYMTDEAVEGRDAFLQKRPPDWSPFPRYF 314
               SCOP domains d1rjnb_ B: Naphthoate synthase MenB                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------1rjnB01 B:21-251 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                              1rjnB02 B:252-302                                  ------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh.eee.........eeeeee....eeeeee.hhhhh...hhhhhhhhhhhhhhhhh.....eeeeee..........eee......--------------------------hhhhhhhhhhhh..eeeeee..eeehhhhhhhhhh.eeeee....eee..hhhhh.......hhhhhhhhhhhhhhhhhhhh.eehhhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rjn B  14 ALSDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQR--------------------------HILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRLAYMTDEAVEGRDAFLQKRPPDWSPFPRYF 314
                                    23        33        43        53        63        73        83        93       103    |    -         -         - |     143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313 
                                                                                                                        108                        135                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:275
 aligned with MENB_MYCTU | P9WNP5 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:301
                                    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       273       283       293       303       313 
           MENB_MYCTU    14 ALSDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQYASGDTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRLAYMTDEAVEGRDAFLQKRPPDWSPFPRYF 314
               SCOP domains d1rjnb_ B: Naphthoate synthase MenB                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------1rjnB01 B:21-251 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                              1rjnB02 B:252-302                                  ------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh.eee.........eeeeee....eeeeee.hhhhh...hhhhhhhhhhhhhhhhh.....eeeeee..........eee......--------------------------hhhhhhhhhhhh..eeeeee..eeehhhhhhhhhh.eeeee....eee..hhhhh.......hhhhhhhhhhhhhhhhhhhh.eehhhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rjn B  14 ALSDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQR--------------------------HILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRLAYMTDEAVEGRDAFLQKRPPDWSPFPRYF 314
                                    23        33        43        53        63        73        83        93       103    |    -         -         - |     143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313 
                                                                                                                        108                        135                                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:245
 aligned with MENB_MYCTO | P9WNP4 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:272
                                    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       273       283  
           MENB_MYCTO    14 ALSDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQYASGDTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRL 285
               SCOP domains d1rjnc_ C: Naphthoate synthase MenB                                                                                                                                                                                                                                              SCOP domains
               CATH domains -------1rjnC01 C:21-251 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                              ---------------------------------- CATH domains
           Pfam domains (1) --------------------------ECH-1rjnC01 C:40-285                                                                                                                                                                                                                                   Pfam domains (1)
           Pfam domains (2) --------------------------ECH-1rjnC02 C:40-285                                                                                                                                                                                                                                   Pfam domains (2)
           Pfam domains (3) --------------------------ECH-1rjnC03 C:40-285                                                                                                                                                                                                                                   Pfam domains (3)
         Sec.struct. author hhhhh..hhh.eee.........eeeeee....eeeeee.hhhhh...hhhhhhhhhhhhhhhhh.....eeeeee..........eee....---------------------------.hhhhhhhhhhhh..eeeeee..eeehhhhhhhhhh.eeeee....eee.hhhhh........hhhhhhhhhhhhhhhhhhhh.eehhhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rjn C  14 ALSDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGD---------------------------LHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRL 285
                                    23        33        43        53        63        73        83        93       103  |      -         -         -|      143       153       163       173       183       193       203       213       223       233       243       253       263       273       283  
                                                                                                                      106                         134                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:245
 aligned with MENB_MYCTU | P9WNP5 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:272
                                    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       273       283  
           MENB_MYCTU    14 ALSDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQYASGDTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRL 285
               SCOP domains d1rjnc_ C: Naphthoate synthase MenB                                                                                                                                                                                                                                              SCOP domains
               CATH domains -------1rjnC01 C:21-251 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                              ---------------------------------- CATH domains
           Pfam domains (1) --------------------------ECH-1rjnC01 C:40-285                                                                                                                                                                                                                                   Pfam domains (1)
           Pfam domains (2) --------------------------ECH-1rjnC02 C:40-285                                                                                                                                                                                                                                   Pfam domains (2)
           Pfam domains (3) --------------------------ECH-1rjnC03 C:40-285                                                                                                                                                                                                                                   Pfam domains (3)
         Sec.struct. author hhhhh..hhh.eee.........eeeeee....eeeeee.hhhhh...hhhhhhhhhhhhhhhhh.....eeeeee..........eee....---------------------------.hhhhhhhhhhhh..eeeeee..eeehhhhhhhhhh.eeeee....eee.hhhhh........hhhhhhhhhhhhhhhhhhhh.eehhhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rjn C  14 ALSDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGD---------------------------LHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRL 285
                                    23        33        43        53        63        73        83        93       103  |      -         -         -|      143       153       163       173       183       193       203       213       223       233       243       253       263       273       283  
                                                                                                                      106                         134
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: ClpP_crotonase (88)
(-)
Family: ECH (52)

(-) Gene Ontology  (7, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (MENB_MYCTU | P9WNP5)
molecular function
    GO:0008935    1,4-dihydroxy-2-naphthoyl-CoA synthase activity    Catalysis of the reaction: 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-napthoyl-CoA + H2O.
    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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0009234    menaquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
    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.
    GO:0034214    protein hexamerization    The formation of a protein hexamer, a macromolecular structure consisting of six noncovalently associated identical or nonidentical subunits.
cellular component
    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,C   (MENB_MYCTO | P9WNP4)
molecular function
    GO:0008935    1,4-dihydroxy-2-naphthoyl-CoA synthase activity    Catalysis of the reaction: 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-napthoyl-CoA + H2O.
    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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0009234    menaquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
    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 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
    COA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EP1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:91 - Pro A:92   [ RasMol ]  
    Gly B:91 - Pro B:92   [ RasMol ]  
    Gly C:91 - Pro C:92   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  1rjn
    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
  MENB_MYCTO | P9WNP4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  MENB_MYCTU | P9WNP5
    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)
  4.1.3.36
    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
  MENB_MYCTO | P9WNP4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MENB_MYCTU | P9WNP5
    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
        MENB_MYCTO | P9WNP4: 1q51 1q52 1rjm 3t8a 3t8b
        MENB_MYCTU | P9WNP5: 1q51 1q52 1rjm 3t8a 3t8b 4qii 4qij

(-) Related Entries Specified in the PDB File

1rjm THE SAME PROTEIN BUT WITH NO LIGAND ASSOCIATED RELATED ID: RV0548C RELATED DB: TARGETDB