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 THE T175V ETR1P MUTANT IN THE TRIGONAL FORM P312 IN COMPLEX WITH NADP AND CROTONYL-COA
 
Authors :  T. Wagner, R. G. Rosenthal, B. Voegeli, S. Shima, T. J. Erb
Date :  17 Jun 16  (Deposition) - 10 May 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Negative Catalysis, Enzyme, Nadp, Mitochondria, Mutant, Crotonyl-Coa, Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. G. Rosenthal, B. Vogeli, T. Wagner, S. Shima, T. J. Erb
A Conserved Threonine Prevents Self-Intoxication Of Enoyl-Thioester Reductases.
Nat. Chem. Biol. V. 13 745 2017
PubMed-ID: 28504678  |  Reference-DOI: 10.1038/NCHEMBIO.2375

(-) Compounds

Molecule 1 - ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH, B-SPECIFIC] 1, MITOCHONDRIAL
    Chains: A, B
    EC Number: 1.3.1.10, 1.3.1.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Plasmid: PTE264
    Expression System Taxid: 866768
    Expression System Vector Type: PLASMID
    Gene: ETR1
    Mutation: YES
    Organism Common: YEAST
    Organism Scientific: CANDIDA TROPICALIS
    Organism Taxid: 5482
    Other Details: THE 20 FIRST RESIDUES ARE NOT VISIBLE IN THE CRYSTAL STRUCTURE. THE SEQUENCE CORRESPONDS TO THE FRAGMENT 23-386 FROM THE ORIGINAL GENE SEQUENCE.
    Synonym: TRANS-2-ENOYL-COA REDUCTASE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2COO2Ligand/IonCROTONYL COENZYME A
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4SO413Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:69 , VAL A:171 , ASN A:172 , VAL A:175 , THR A:199 , SER A:200 , ALA A:201 , VAL A:202 , ARG A:222 , ARG A:224 , TYR A:296 , GLY A:297 , MET A:299 , PHE A:321 , VAL A:323 , LYS A:381 , COO A:410 , HOH A:527 , HOH A:534 , HOH A:573binding site for residue NAP A 401
02AC2SOFTWARESER A:125 , HIS A:126 , VAL A:127 , LYS A:331binding site for residue SO4 A 402
03AC3SOFTWARESER A:250 , ARG A:251 , GLU A:252binding site for residue SO4 A 403
04AC4SOFTWAREVAL A:242 , GLN A:247binding site for residue SO4 A 404
05AC5SOFTWARELYS A:145 , GLN A:151 , ASN A:155binding site for residue SO4 A 405
06AC6SOFTWAREGLN A:33 , HIS A:34 , LYS A:85 , HOH A:544binding site for residue SO4 A 406
07AC7SOFTWAREARG A:224 , ASN A:226binding site for residue SO4 A 407
08AC8SOFTWARELYS B:278 , ARG B:285binding site for residue SO4 A 408
09AC9SOFTWAREASN A:288 , ASN A:289binding site for residue SO4 A 409
10AD1SOFTWARESER A:70 , ASN A:73 , TYR A:79 , GLY A:297 , GLY A:298 , THR A:324 , NAP A:401 , HOH A:569 , THR B:308 , SER B:309binding site for residue COO A 410
11AD2SOFTWARELYS A:153binding site for residue CL A 411
12AD3SOFTWAREVAL B:171 , ASN B:172 , VAL B:175 , THR B:199 , SER B:200 , ALA B:201 , VAL B:202 , ARG B:222 , ARG B:224 , TYR B:296 , GLY B:297 , MET B:299 , PHE B:321 , VAL B:323 , LYS B:381 , COO B:407 , HOH B:528 , HOH B:541 , HOH B:551 , HOH B:553binding site for residue NAP B 401
13AD4SOFTWAREGLN B:33 , HIS B:34 , LYS B:85binding site for residue SO4 B 402
14AD5SOFTWAREVAL B:242 , GLN B:247binding site for residue SO4 B 403
15AD6SOFTWAREARG B:224 , ASN B:226 , VAL B:230binding site for residue SO4 B 404
16AD7SOFTWAREARG B:222 , LYS B:378binding site for residue SO4 B 405
17AD8SOFTWAREASN B:288 , ASN B:289 , HOH B:504binding site for residue SO4 B 406
18AD9SOFTWARETHR A:308 , SER A:309 , SER B:70 , ASN B:73 , TYR B:79 , GLY B:298 , MET B:299 , PHE B:301 , THR B:324 , NAP B:401 , HOH B:503binding site for residue COO B 407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LBX)

(-) 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:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhheeeeeeee.......eeeeeeeeeeehhhhhhhhhh..................ee.....eeeeeee...........eeee..........eeeee...eeee.hhhhhhhh......hhhhhhh..hhhhhhhhhhhh.........eeee....hhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhh...eeeeee..hhhhhhhhhhh.....eeee........eeehhhhhhhh..eeee.hhhhhh..hhhhhhhhhhhhhhhhhh........eeee.....hhhhhhhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lbx A  22 HMITAQAVLYTQHGEPKDVLFTQSFEIDDDNLAPNEVIVKTLGSPVNPSDINQIQGVYPSKPAKTTGFGTTEPAAPCGNEGLFEVIKVGSNVSSLEAGDWVIPSHVNFGTWRTHALGNDDDFIKLPNPAQSKANGKPNGLTINQGATISVNPLVAYLMLTHYVKLTPGKDWFIQNGGTSAVGKYASQIGKLLNFNSISVIRDRPNLDEVVASLKELGATQVITEDQNNSREFGPTIKEWIKQSGGEAKLALNCVGGKSSTGIARKLNNNGLMLTYGGMSFQPVTIPTSLYIFKNFTSAGFWVTELLKNNKELKTSTLNQIIAWYEEGKLTDAKSIETLYDGTKPLHELYQDGVANSKDGKQLITY 386
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381     


Chain B from PDB  Type:PROTEIN  Length:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhheeeeeeee.......eeeeeeeeeeehhhhhhhhhh..................ee.....eeeeeee...........eeee..........eeeee...eeee.hhhhhhhh......hhhhhhh..hhhhhhhhhhhh.........eeeee...hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh.....eeee........eeehhhhhhhhh.eeee.hhhhhh..hhhhhhhhhhhhhhhhhh........eeee.....hhhhhhhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lbx B  22 HMITAQAVLYTQHGEPKDVLFTQSFEIDDDNLAPNEVIVKTLGSPVNPSDINQIQGVYPSKPAKTTGFGTTEPAAPCGNEGLFEVIKVGSNVSSLEAGDWVIPSHVNFGTWRTHALGNDDDFIKLPNPAQSKANGKPNGLTINQGATISVNPLVAYLMLTHYVKLTPGKDWFIQNGGTSAVGKYASQIGKLLNFNSISVIRDRPNLDEVVASLKELGATQVITEDQNNSREFGPTIKEWIKQSGGEAKLALNCVGGKSSTGIARKLNNNGLMLTYGGMSFQPVTIPTSLYIFKNFTSAGFWVTELLKNNKELKTSTLNQIIAWYEEGKLTDAKSIETLYDGTKPLHELYQDGVANSKDGKQLITY 386
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381
   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 5LBX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    COO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5lbx)
 

(-) 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
  5lbx
    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
  ETR1_CANTR | Q8WZM3
    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)
  1.3.1.10
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  1.3.1.38
    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
  ETR1_CANTR | Q8WZM3
    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
        ETR1_CANTR | Q8WZM3: 1gu7 1guf 1gyr 1n9g 4w99 4was 5lb9

(-) Related Entries Specified in the PDB File

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