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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF RV2671 FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH THE TETRAHYDROPTERIDINE RING OF TETRAHYDROFOLATE (THF)
 
Authors :  J. C. Sacchettini, Y. S. Cheng, Tb Structural Genomics Consortium
Date :  23 Jan 15  (Deposition) - 24 Feb 16  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tetrahydrofolate (Thf), Reductase, Nadp+, Structural Genomics, Tb Structural Genomics Consortium, Tbsgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. S. Cheng, J. C. Sacchettini
Structural Insights Into Mycobacterium Tuberculosis Rv2671 Protein As A Dihydrofolate Reductase Functional Analogue Contributing To Para-Aminosalicylic Acid Resistance.
Biochemistry V. 55 1107 2016
PubMed-ID: 26848874  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00993

(-) Compounds

Molecule 1 - RV2671
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RIBD, RV2671, RVBD_2671, LH57_14640, P425_02787
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
144V1Ligand/Ion(6S)-2-AMINO-6-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-4(3H)-ONE
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
144V2Ligand/Ion(6S)-2-AMINO-6-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-4(3H)-ONE
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:84 , VAL A:85 , GLY A:86 , THR A:87 , VAL A:120 , THR A:121 , ARG A:122 , SER A:123 , VAL A:173 , GLU A:175 , GLY A:195 , PRO A:196 , THR A:197 , LEU A:198 , THR A:201 , HOH A:462binding site for residue NAP A 301
2AC2SOFTWAREASN A:44 , PHE A:45 , ILE A:46 , SER A:59 , ASP A:67 , GLU A:193 , THR A:214 , HOH A:436 , HOH A:457binding site for residue 44V A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XT6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:194 -Gly A:195
2Lys A:257 -Thr A:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XT6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XT6)

(-) Exons   (0, 0)

(no "Exon" information available for 4XT6)

(-) 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:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh.......eeeeeeeee........hhhhhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhh......eeeee.........hhhhhh.....eeeehhhhhhhhhhhh....eeee.........hhhhhhhhhhh....eeeeeehhhhhhhhhhh....eeeeeee.....................eeeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xt6 A  13 PLRLLSSVHYLTGELPQLYDYPDDGTWLRANFISSLDGGATVTSGAMAGPGDRFVFNLLRELADVIVVGVGTVRVRMGVVQRQHRQARGQSEVPQLAIVTRSGRLDRDMAVFTRTEMAPLVLTTTAVADDTRQRLAGLAEVIACSGDDPGTVDEAVLVSQLAARGLRRILTEGGPTLLGTFVERDVLDELCLTIAPYVVGGLARRIVTGPGQVLTRMRCAHVLTDDSGYLYTRYVKT 258
                                    22 ||     33        43        53 ||     65        75        85   ||  101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
                                      24|                           55|                             89|                                                                                                                                                                  
                                       26                            58                              96
   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 4XT6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XT6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XT6)

(-) Gene Ontology  (4, 4)

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
    44V  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:194 - Gly A:195   [ RasMol ]  
    Lys A:257 - Thr A:258   [ 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
  4xt6
    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
  A0A089S8V3_M | A0A089S8V3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  P71968_MYCTU | P71968
    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
  A0A089S8V3_M | A0A089S8V3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  P71968_MYCTU | P71968
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A0A089S8V3_M | A0A089S8V3: 4xrb 4xt4 4xt5 4xt7 4xt8
        P71968_MYCTU | P71968: 4xrb 4xt4 4xt5 4xt7 4xt8

(-) Related Entries Specified in the PDB File

4xrb 4xt4 4xt5 4xt7 4xt8