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

(-) Description

Title :  CRYSTAL STRUCTURE OF A DTDP-4-DEHYDRORHAMNOSE REDUCTASE, RFBD ORTHOLOG (CA_C2315) FROM CLOSTRIDIUM ACETOBUTYLICUM ATCC 824 AT 2.05 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  30 Jun 04  (Deposition) - 17 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dtdp-4-Dehydrorhamnose Reductase, Rfbd Ortholog, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Dtdp-4-Dehydrorhamnose Reductase, Rfbd Ortholog (Cac2315) From Clostridium Acetobutylicum At 2. 05 Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DTDP-4-DEHYDRORHAMNOSE REDUCTASE, RFBD ORTHOLOG
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CAC2315
    Organism Scientific: CLOSTRIDIUM ACETOBUTYLICUM
    Organism Taxid: 272562
    Strain: ATCC 824

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2NAI3Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3UNL1Ligand/IonUNKNOWN LIGAND

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , GLN A:11 , LEU A:12 , ASP A:31 , LEU A:35 , ASP A:36 , ILE A:37 , CYS A:58 , ALA A:59 , ALA A:60 , THR A:62 , ILE A:99 , SER A:100 , THR A:101 , TYR A:125 , LYS A:129 , THR A:148 , TRP A:150 , LEU A:151 , HOH A:313 , HOH A:383BINDING SITE FOR RESIDUE NAI A 300
2AC2SOFTWARETHR A:207 , CYS A:208 , GLY A:210 , ILE A:211 , LEU A:251 , ARG A:252 , ASN A:253 , HOH A:309 , HOH A:324 , HOH A:337BINDING SITE FOR RESIDUE UNL A 301
3AC3SOFTWAREGLY B:10 , GLN B:11 , LEU B:12 , ASP B:31 , VAL B:32 , LEU B:35 , ASP B:36 , ILE B:37 , CYS B:58 , ALA B:59 , ALA B:60 , THR B:62 , ILE B:77 , ILE B:99 , SER B:100 , THR B:101 , TYR B:125 , LYS B:129 , THR B:148 , LEU B:151 , HOH B:306 , HOH B:309 , HOH B:349 , HOH B:360 , HOH B:445BINDING SITE FOR RESIDUE NAI B 300
4AC4SOFTWAREGLY C:10 , GLN C:11 , LEU C:12 , ASP C:31 , VAL C:32 , LEU C:35 , ASP C:36 , ILE C:37 , CYS C:58 , ALA C:59 , ALA C:60 , THR C:62 , ILE C:99 , SER C:100 , THR C:101 , TYR C:125 , LYS C:129 , THR C:148 , TRP C:150 , LEU C:151 , HOH C:306 , HOH C:310 , HOH C:318 , HOH C:394BINDING SITE FOR RESIDUE NAI C 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VL0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VL0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VL0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VL0)

(-) Exons   (0, 0)

(no "Exon" information available for 1VL0)

(-) 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:281
 aligned with Q97GQ1_CLOAB | Q97GQ1 from UniProtKB/TrEMBL  Length:280

    Alignment length:281
                             1                                                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279 
         Q97GQ1_CLOAB     - -MKILITGANGQLGREIQKQLKGKNVEVIPTDVQDLDITNVLAVNKFFNEKKPNVVINCAAHTAVDKCEEQYDLAYKINAIGPKNLAAAAYSVGAEIVQISTDYVFDGEAKEPITEFDEVNPQSAYGKTKLEGENFVKALNPKYYIVRTAWLYGDGNNFVKTMINLGKTHDELKVVHDQVGTPTSTVDLARVVLKVIDEKNYGTFHCTCKGICSWYDFAVEIFRLTGIDVKVTPCTTEEFPRPAKRPKYSVLRNYMLELTTGDITREWKESLKEYIDLLQM 280
               SCOP domains d1vl0a_ A: DTDP-4-dehydrorhamnose reductase RfbD                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1vl0A01 A:0-157,A:181-209,A:250-265 NAD(P)-binding Rossmann-like Domain                                                                                       -----------------------1vl0A01                      ----------------------------------------1vl0A01         --------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhh.................hhhhhhhhhhhhhhhhhh..eeeeee..ee....hhhhhhhhhhhhh.eeeee...ee..eehhhhhhhhhhhhhhh..eeee......eehhhhhhhhhhhhh...eeeee..................hhhhhhh......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vl0 A   0 HmKILITGANGQLGREIQKQLKGKNVEVIPTDVQDLDITNVLAVNKFFNEKKPNVVINCAAHTAVDKCEEQYDLAYKINAIGPKNLAAAAYSVGAEIVQISTDYVFDGEAKEPITEFDEVNPQSAYGKTKLEGENFVKALNPKYYIVRTAWLYGDGNNFVKTmINLGKTHDELKVVHDQVGTPTSTVDLARVVLKVIDEKNYGTFHCTCKGICSWYDFAVEIFRLTGIDVKVTPCTTEEFPRPAKRPKYSVLRNYmLELTTGDITREWKESLKEYIDLLQm 280
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159  |    169       179       189       199       209       219       229       239       249     | 259       269       279|
                             |                                                                                                                                                              162-MSE                                                                                      255-MSE                  280-MSE
                             1-MSE                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:280
 aligned with Q97GQ1_CLOAB | Q97GQ1 from UniProtKB/TrEMBL  Length:280

    Alignment length:280
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280
         Q97GQ1_CLOAB     1 MKILITGANGQLGREIQKQLKGKNVEVIPTDVQDLDITNVLAVNKFFNEKKPNVVINCAAHTAVDKCEEQYDLAYKINAIGPKNLAAAAYSVGAEIVQISTDYVFDGEAKEPITEFDEVNPQSAYGKTKLEGENFVKALNPKYYIVRTAWLYGDGNNFVKTMINLGKTHDELKVVHDQVGTPTSTVDLARVVLKVIDEKNYGTFHCTCKGICSWYDFAVEIFRLTGIDVKVTPCTTEEFPRPAKRPKYSVLRNYMLELTTGDITREWKESLKEYIDLLQM 280
               SCOP domains d1vl0b_ B: DTDP-4-dehydrorhamnose reductase RfbD                                                                                                                                                                                                                                         SCOP domains
               CATH domains -1vl0B01 B:2-157,B:181-209,B:250-265 NAD(P)-binding Rossmann-like Domain                                                                                     -----------------------1vl0B01                      ----------------------------------------1vl0B01         --------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhh....eeeee........hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhh.................hhhhhhhhhhhhhhhhhh..eeeeee..ee....hhhhhhhhhhhhh.eeeee...ee..eehhhhhhhhhhhhhhh..eeee......eehhhhhhhhhhhhh...eeeeehhhhh.............hhhhhhh......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vl0 B   1 mKILITGANGQLGREIQKQLKGKNVEVIPTDVQDLDITNVLAVNKFFNEKKPNVVINCAAHTAVDKCEEQYDLAYKINAIGPKNLAAAAYSVGAEIVQISTDYVFDGEAKEPITEFDEVNPQSAYGKTKLEGENFVKALNPKYYIVRTAWLYGDGNNFVKTmINLGKTHDELKVVHDQVGTPTSTVDLARVVLKVIDEKNYGTFHCTCKGICSWYDFAVEIFRLTGIDVKVTPCTTEEFPRPAKRPKYSVLRNYmLELTTGDITREWKESLKEYIDLLQm 280
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 |     170       180       190       200       210       220       230       240       250    |  260       270       280
                            |                                                                                                                                                              162-MSE                                                                                      255-MSE                  280-MSE
                            1-MSE                                                                                                                                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:281
 aligned with Q97GQ1_CLOAB | Q97GQ1 from UniProtKB/TrEMBL  Length:280

    Alignment length:281
                             1                                                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279 
         Q97GQ1_CLOAB     - -MKILITGANGQLGREIQKQLKGKNVEVIPTDVQDLDITNVLAVNKFFNEKKPNVVINCAAHTAVDKCEEQYDLAYKINAIGPKNLAAAAYSVGAEIVQISTDYVFDGEAKEPITEFDEVNPQSAYGKTKLEGENFVKALNPKYYIVRTAWLYGDGNNFVKTMINLGKTHDELKVVHDQVGTPTSTVDLARVVLKVIDEKNYGTFHCTCKGICSWYDFAVEIFRLTGIDVKVTPCTTEEFPRPAKRPKYSVLRNYMLELTTGDITREWKESLKEYIDLLQM 280
               SCOP domains d1vl0c_ C: DTDP-4-dehydrorhamnose reductase RfbD                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1vl0C01 C:0-157,C:181-209,C:250-265 NAD(P)-binding Rossmann-like Domain                                                                                       -----------------------1vl0C01                      ----------------------------------------1vl0C01         --------------- CATH domains
           Pfam domains (1) -RmlD_sub_bind-1vl0C01 C:1-280                                                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) -RmlD_sub_bind-1vl0C02 C:1-280                                                                                                                                                                                                                                                            Pfam domains (2)
           Pfam domains (3) -RmlD_sub_bind-1vl0C03 C:1-280                                                                                                                                                                                                                                                            Pfam domains (3)
         Sec.struct. author .eeeeee...hhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhh.................hhhhhhhhhhhhhhhhhh..eeeeee..ee....hhhhhhhhhhhhh.eeeee...ee..eehhhhhhhhhhhhhhh..eeee......eehhhhhhhhhhhhh...eeeeehhhhh.............hhhhhhh......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vl0 C   0 HmKILITGANGQLGREIQKQLKGKNVEVIPTDVQDLDITNVLAVNKFFNEKKPNVVINCAAHTAVDKCEEQYDLAYKINAIGPKNLAAAAYSVGAEIVQISTDYVFDGEAKEPITEFDEVNPQSAYGKTKLEGENFVKALNPKYYIVRTAWLYGDGNNFVKTmINLGKTHDELKVVHDQVGTPTSTVDLARVVLKVIDEKNYGTFHCTCKGICSWYDFAVEIFRLTGIDVKVTPCTTEEFPRPAKRPKYSVLRNYmLELTTGDITREWKESLKEYIDLLQm 280
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159  |    169       179       189       199       209       219       229       239       249     | 259       269       279|
                             |                                                                                                                                                              162-MSE                                                                                      255-MSE                  280-MSE
                             1-MSE
   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  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q97GQ1_CLOAB | Q97GQ1)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vl0)
 

(-) 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
  1vl0
    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
  Q97GQ1_CLOAB | Q97GQ1
    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)
  (no 'Enzyme Classificator' available)
    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
  Q97GQ1_CLOAB | Q97GQ1
    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 1VL0)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VL0)