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 :  BINDING OF NB113 CAMELID ANTIBODY FRAGMENT WITH THE BINARY DHFR:FOLATE COMPLEX
 
Authors :  D. Oyen, V. Srinivasan
Date :  06 Apr 12  (Deposition) - 24 Apr 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Folate, Oxidoreductase-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Oyen, R. Wechselberger, V. Srinivasan, J. Steyaert, J. N. Barlow
Mechanistic Analysis Of Allosteric And Non-Allosteric Effects Arising From Nanobody Binding To Two Epitopes Of Th Dihyrofolate Reductase Of Escherichia Coli.
Biochim. Biophys. Acta V. 1834 2147 2013
PubMed-ID: 23911607  |  Reference-DOI: 10.1016/J.BBAPAP.2013.07.010

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: A, B
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FOLA, TMRA, B0048, JW0047
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
 
Molecule 2 - NB113 CAMELID ANTIBODY FRAGMENT
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1FOL2Ligand/IonFOLIC ACID
2PO46Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FOL1Ligand/IonFOLIC ACID
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1FOL1Ligand/IonFOLIC ACID
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:5 , ALA A:6 , ALA A:7 , GLU A:17 , ASP A:27 , LEU A:28 , PHE A:31 , LYS A:32 , ILE A:50 , ARG A:52 , ARG A:57 , ILE A:94 , TYR A:100 , THR A:113 , HOH A:302 , HOH A:349 , HOH A:350 , HOH A:391 , HOH A:410BINDING SITE FOR RESIDUE FOL A 201
2AC2SOFTWAREGLY A:43 , ARG A:44 , HIS A:45 , THR A:46 , GLY A:96 , HOH A:325 , HOH A:365 , HOH A:417BINDING SITE FOR RESIDUE PO4 A 202
3AC3SOFTWAREARG A:44 , SER A:63 , SER A:64 , HOH A:371 , HOH A:417BINDING SITE FOR RESIDUE PO4 A 203
4AC4SOFTWAREASP A:144 , ALA A:145 , GLN A:146 , LYS C:76 , HOH C:315BINDING SITE FOR RESIDUE PO4 A 204
5AC5SOFTWAREILE B:5 , ALA B:6 , ALA B:7 , GLU B:17 , ASP B:27 , PHE B:31 , LYS B:32 , LEU B:54 , ARG B:57 , ILE B:94 , TYR B:100 , THR B:113 , HOH B:303 , HOH B:308 , HOH B:403 , HOH B:427BINDING SITE FOR RESIDUE FOL B 201
6AC6SOFTWAREGLY B:43 , ARG B:44 , HIS B:45 , THR B:46 , GLY B:96 , VAL B:99 , HOH B:361 , HOH B:429BINDING SITE FOR RESIDUE PO4 B 202
7AC7SOFTWAREARG B:44 , SER B:63 , SER B:64 , ARG B:98 , ARG D:27BINDING SITE FOR RESIDUE PO4 B 203
8AC8SOFTWAREASP B:144 , ALA B:145 , GLN B:146 , LYS D:76BINDING SITE FOR RESIDUE PO4 B 204

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1C:22 -C:96
2D:22 -D:96

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:95 -Gly A:96
2Gly B:95 -Gly B:96
3Arg C:27 -Thr C:28

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EJ1)

(-) Exons   (0, 0)

(no "Exon" information available for 4EJ1)

(-) 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:159
                                                                                                                                                                                               
               SCOP domains d4ej1a_ A: Dihydrofolate reductase, prokaryotic type                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhh..hhhhh...hhhhhhhhhhhhh...eeeehhhhhhhh.......eeee..........eee.hhhhhhhhh.....eee..hhhhhhhhhhhh.eeeeeee.................eeeeeeeee.........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ej1 A   1 MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         


Chain B from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains d4ej1b_ B: Dihydrofolate reductase, prokaryotic type                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhh..........hhhhhhhhhhhhh...eeeehhhhhhhh.......eeee..........eee.hhhhhhhhh.....eee..hhhhhhhhhhhh.eeeeeee.................eeeeeeeee.........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ej1 B   1 MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         


Chain C from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains d4ej1c_ C: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee...eee....eeeeeee.........eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.....hhhhhhhh..eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ej1 C   3 QLQESGGGLVQAGGSLRLSCTASGRTFSSYAMGWFRQTPGKEREFVAAITWGGSTTLYADSVKGRFTMSRDNAKNTVYLQMNSLKPEDTAVYYCAADGSQYRSTYSFRDKPDYGSWGQGTQVTVSS 128
                                    12        22        32        42        52        62        72        82        92       102       112       122      


Chain D from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains d4ej1d_ D: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eee.....eeeeeee...hhhhh.eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.....hhhhhhhh..eeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ej1 D   3 QLQESGGGLVQAGGSLRLSCTASGRTFSSYAMGWFRQTPGKEREFVAAITWGGSTTLYADSVKGRFTMSRDNAKNTVYLQMNSLKPEDTAVYYCAADGSQYRSTYSFRDKPDYGSWGQGTQVTVSS 128
                                    12        22        32        42        52        62        72        82        92       102       112       122
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EJ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EJ1)

(-) Gene Ontology  (13, 13)

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
    FOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 ]
 
  Cis Peptide Bonds
    Arg C:27 - Thr C:28   [ RasMol ]  
    Gly A:95 - Gly A:96   [ RasMol ]  
    Gly B:95 - Gly B:96   [ RasMol ]  
 
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
  4ej1
    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
  DYR_ECOLI | P0ABQ4
    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)
  1.5.1.3
    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
  DYR_ECOLI | P0ABQ4
    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
        DYR_ECOLI | P0ABQ4: 1ddr 1dds 1dhi 1dhj 1dra 1drb 1dre 1drh 1dyh 1dyi 1dyj 1jol 1jom 1ra1 1ra2 1ra3 1ra8 1ra9 1rb2 1rb3 1rc4 1rd7 1re7 1rf7 1rg7 1rh3 1rx1 1rx2 1rx3 1rx4 1rx5 1rx6 1rx7 1rx8 1rx9 1tdr 2ano 2anq 2d0k 2drc 2inq 3dau 3drc 3k74 3kfy 3och 3ql3 3qyl 3qyo 3r33 4dfr 4eig 4eiz 4fhb 4gh8 4i13 4i1n 4kjj 4kjk 4kjl 4nx6 4nx7 4pdj 4x5f 4x5g 4x5h 4x5i 4x5j 5cc9 5ccc 5dfr 5e8q 5eaj 6dfr 7dfr

(-) Related Entries Specified in the PDB File

4eig 4eiz