Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF FADD32 FROM MYCOBACTERIUM MARINUM COMPLEXED TO AMPC12
 
Authors :  V. Guillet, L. Maveyraud, L. Mourey
Date :  24 Nov 15  (Deposition) - 16 Dec 15  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ligase, Fatty-Acyl Amp Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Guillet, S. Galandrin, L. Maveyraud, S. Ladeveze, V. Mariaule, C. Bon, N. Eynard, M. Daffe, H. Marrakchi, L. Mourey
Insight Into Structure-Function Relationships And Inhibitio Of The Fatty Acyl-Amp Ligase (Fadd32) Orthologs From Mycobacteria.
J. Biol. Chem. V. 291 7973 2016
PubMed-ID: 26900152  |  Reference-DOI: 10.1074/JBC.M115.712612

(-) Compounds

Molecule 1 - LONG-CHAIN-FATTY-ACID--AMP LIGASE FADD32
    Chains: A, B
    EC Number: 6.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FADD32, MMAR_5365
    Organism Scientific: MYCOBACTERIUM MARINUM
    Organism Taxid: 1781
    Synonym: FAAL,ACYL-AMP SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
15SV2Ligand/Ion[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL ICOSYL HYDROGENPHOSPHATE
2GOL7Ligand/IonGLYCEROL
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
15SV1Ligand/Ion[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL ICOSYL HYDROGENPHOSPHATE
2GOL4Ligand/IonGLYCEROL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
15SV1Ligand/Ion[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL ICOSYL HYDROGENPHOSPHATE
2GOL3Ligand/IonGLYCEROL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:230 , ASP A:231 , MET A:232 , SER A:278 , LEU A:310 , SER A:313 , GLU A:314 , PRO A:315 , SER A:341 , TYR A:342 , GLY A:343 , LEU A:344 , ALA A:345 , LEU A:349 , ASP A:468 , ILE A:479 , ARG A:482 , LYS A:600 , HOH A:869 , HOH A:915 , HOH A:976 , HOH A:984binding site for residue 5SV A 701
2AC2SOFTWAREASP A:397 , GLU A:398 , TRP A:399 , HOH A:871binding site for residue GOL A 702
3AC3SOFTWAREASP A:413 , PHE A:473 , LYS A:474binding site for residue GOL A 703
4AC4SOFTWAREARG A:268 , THR A:273 , GLY A:274 , SER A:304 , ASN A:305binding site for residue GOL A 704
5AC5SOFTWAREVAL A:156 , ILE A:157 , ALA A:158 , ALA A:161 , VAL A:162 , VAL B:378 , ALA B:382 , HOH B:832binding site for residue GOL A 705
6AC6SOFTWAREVAL B:210 , HIS B:230 , ASP B:231 , THR B:236 , SER B:278 , LEU B:310 , SER B:313 , GLU B:314 , PRO B:315 , SER B:341 , TYR B:342 , GLY B:343 , LEU B:344 , LEU B:349 , ASP B:468 , ILE B:479 , ARG B:482 , LYS B:600 , HOH B:846 , HOH B:882 , HOH B:977 , HOH B:982binding site for residue 5SV B 701
7AC7SOFTWAREGLY B:395 , ASP B:397 , GLU B:398 , TRP B:399 , HOH B:889binding site for residue GOL B 702
8AC8SOFTWAREASP B:413 , PHE B:473 , LYS B:474binding site for residue GOL B 703
9AC9SOFTWAREGLU B:139 , ARG B:268 , THR B:273 , GLY B:274 , ASN B:305 , ARG B:334binding site for residue GOL B 704

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EY9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EY9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EY9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EY9)

(-) Exons   (0, 0)

(no "Exon" information available for 5EY9)

(-) 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:610
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..ee......hhhhhhhhhhhhh...eeeeeee.......eeeeeehhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhh..eeeehhhhhhhhhhhhhh.......eeee.hhhhhhhhhhh.......eeeeee....eeeee.hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhh........eeeeehhhhhhhhhhhh.............eeeeee.....hhhhhhhhhhhhhhhh.....eeeeee.hhhh.eeee........eeeeehhhhhh............eeeee...ee...eeeeeee....ee......eeeeeee.........hhhhhhhhhhee.................eeeeeeeeeeee..eeeeeee.hhheee..eeehhhhhhhhhhhh...eeeeeeeeeeee.hhhhhhhhhh.............eeeeeeeee.......hhhhhhhhhhhhhhhhhh..eeeeeee.............hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ey9 A   3 YHNPFIVNGKIRFPENTNLVRHVEKWARVRGDKLAYRFLDFSTERDGVERDILWSEFSARNRAVGARLQQVTQPGDRIAILCPQNLDYLISFFGALYSGRIAVPLFDPAEHVGRLHAVLDDCTPSTILTTTDSAEGVRKFIRSRSAKERPRVIAVDAVPTEVASTWQQPNELTTAYLQYTVPSGVQITHLNLPTNVLQVLNALEGQEGDRGVSWLPFFHDMGLITVLLASVLGHSFTFMTPAAFVRRPGRWIRELARKPGETGGTFSAAPNFAFEHAAMRGVPRDDEPPLDLSNVKGILNGSEPVSPASMRKFFKAFEPYGLRETAVKPSYGLAEATLFVSTTPMDEVPTVIHVDRDELNKQRFVEVAADAPNAVAQVSAGKVGVDEWAVIVDTETASELPDGQIGEIWLHGNNLGIGYWGKEEESAQTFRNILKSRVPESHAEGAPDDGLWVRTGDYGTYFKGHLYIAGRIKDLVIIDGRNHYPQDLEYTAQESTKALRVGYVAAFSVPANQLPQKVFDDPHAGLSFDPEDTSEQLVIVGERAAGTHKLEYQPIADDIRAAIAVGHGVTVRDVLLVSAGTIPRTSSGKIGRRACRTAYIDGSLRSTVFA 626
                                    12        22        32        42        52        62        72        82        92       102       112|      124       134       144       154       164       176       186|      201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611     ||626
                                                                                                                                       112|                                                       173|       186|                                                                                                                                                                                                                                                                                                                                                                                                                                      617|   
                                                                                                                                        115                                                        176        192                                                                                                                                                                                                                                                                                                                                                                                                                                       623   


Chain B from PDB  Type:PROTEIN  Length:610
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..ee......hhhhhhhhhhhhh...eeeeeee.......eeeeeehhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhh..eeeehhhhhhhhhhhhhh.......eeee.hhhhhhhhhhh.........eeeeee....eeeee.hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhh........eeeeehhhhhhhhhhhh.............eeeeee.....hhhhhhhhhhhhhhhh.....eeeeee.hhhh.eeee........eeeeehhhhhh............eeeee...ee...eeeeeee....ee......eeeeeee.........hhhhhhhhhhee.................eeeeeeeeeeee..eeeeeee.hhhee....eehhhhhhhhhhhh...eeeeeeeeeeee.hhhhhhhhhh.............eeeeeeeee.......hhhhhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ey9 B   3 YHNPFIVNGKIRFPENTNLVRHVEKWARVRGDKLAYRFLDFSTERDGVERDILWSEFSARNRAVGARLQQVTQPGDRIAILCPQNLDYLISFFGALYSGRIAVPLFDPAEHVGRLHAVLDDCTPSTILTTTDSAEGVRKFIRSRSAKERPRVIAVDAVPTEVASTWQQPEANELTTAYLQYTVPSGVQITHLNLPTNVLQVLNALEGQEGDRGVSWLPFFHDMGLITVLLASVLGHSFTFMTPAAFVRRPGRWIRELARKPGETGGTFSAAPNFAFEHAAMRGVPRDDEPPLDLSNVKGILNGSEPVSPASMRKFFKAFEPYGLRETAVKPSYGLAEATLFVSTTPMDEVPTVIHVDRDELNKQRFVEVAADAPNAVAQVSAGKVGVDEWAVIVDTETASELPDGQIGEIWLHGNNLGIGYWGKEEESAQTFRNILKSRVPESHAEGAPDDGLWVRTGDYGTYFKGHLYIAGRIKDLVIIDGRNHYPQDLEYTAQESTKALRVGYVAAFSVPANQLPQKVFDDPHAGLSFDPEDTSEQLVIVGERAAGTHKLEYQPIADDIRAAIAVGHGVTVRDVLLVSAGTIPRTSSGKIGRRACRTAYIDGSLRTVF 625
                                    12        22        32        42        52        62        72        82        92       102       112|      124       134       144       154       164       174       184 ||    199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609      |625
                                                                                                                                       112|                                                                    186|                                                                                                                                                                                                                                                                                                                                                                                                                                     616|  
                                                                                                                                        115                                                                     192                                                                                                                                                                                                                                                                                                                                                                                                                                      623
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5EY9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EY9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EY9)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    5SV  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ey9)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5ey9
    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
  FAA32_MYCMM | B2HMK0
    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)
  6.2.1.-
    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
  FAA32_MYCMM | B2HMK0
    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 5EY9)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5EY9)