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 A MESO-DIAMINOPIMELATE DEHYDROGENASE IN COMPLEX WITH NADP
 
Authors :  H. Sakuraba, H. Akita, T. Ohshima
Date :  25 Aug 14  (Deposition) - 06 May 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Akita, T. Seto, T. Ohshima, H. Sakuraba
Structural Insight Into The Thermostable Nadp(+)-Dependent Meso-Diaminopimelate Dehydrogenase From Ureibacillus Thermosphaericus
Acta Crystallogr. , Sect. D V. 71 1136 2015
PubMed-ID: 25945579  |  Reference-DOI: 10.1107/S1399004715003673

(-) Compounds

Molecule 1 - MESO-DIAMINOPIMELATE D-DEHYDROGENASE
    Chains: A, B
    EC Number: 1.4.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DDH
    Organism Scientific: UREIBACILLUS THERMOSPHAERICUS
    Organism Taxid: 51173
    Synonym: DAPDH, MESO-DAP DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2NES4Ligand/Ion2-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-ETHANESULFONIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , TYR A:11 , GLY A:12 , ASN A:13 , LEU A:14 , THR A:35 , ARG A:36 , ARG A:37 , CYS A:69 , GLY A:70 , GLY A:71 , SER A:72 , ASP A:75 , SER A:92 , ASP A:94 , VAL A:121 , TRP A:123 , ASP A:124 , PRO A:125 , ASN A:276 , THR A:280 , NES A:1002 , HOH A:1107 , HOH A:1113 , HOH A:1115 , HOH A:1120 , HOH A:1125 , HOH A:1137 , HOH A:1142 , HOH A:1147 , HOH A:1173 , HOH A:1204 , HOH A:1236 , HOH A:1272 , HOH A:1275 , LYS B:213BINDING SITE FOR RESIDUE NAP A 1001
2AC2SOFTWARETRP A:123 , ASP A:124 , TRP A:148 , SER A:153 , HIS A:156 , THR A:173 , ARG A:199 , HIS A:249 , NAP A:1001 , HOH A:1139 , HOH A:1183 , HOH A:1239BINDING SITE FOR RESIDUE NES A 1002
3AC3SOFTWAREVAL A:53 , ASP A:54 , GLU A:78 , GLN A:79 , TYR A:82 , HOH A:1228BINDING SITE FOR RESIDUE NES A 1003
4AC4SOFTWARELYS A:213 , GLY B:10 , TYR B:11 , GLY B:12 , ASN B:13 , LEU B:14 , THR B:35 , ARG B:36 , ARG B:37 , CYS B:69 , GLY B:70 , GLY B:71 , SER B:72 , ASP B:75 , SER B:92 , ASP B:94 , VAL B:121 , TRP B:123 , ASP B:124 , PRO B:125 , ASN B:276 , THR B:280 , NES B:1002 , HOH B:1104 , HOH B:1112 , HOH B:1115 , HOH B:1121 , HOH B:1131 , HOH B:1133 , HOH B:1137 , HOH B:1225 , HOH B:1232 , HOH B:1234 , HOH B:1251 , HOH B:1252BINDING SITE FOR RESIDUE NAP B 1001
5AC5SOFTWARETRP B:123 , ASP B:124 , TRP B:148 , SER B:153 , HIS B:156 , THR B:173 , ARG B:199 , HIS B:249 , NAP B:1001 , HOH B:1147 , HOH B:1227BINDING SITE FOR RESIDUE NES B 1002
6AC6SOFTWAREVAL B:53 , ASP B:54 , GLU B:78 , GLN B:79 , TYR B:82 , PHE B:83 , HOH B:1207BINDING SITE FOR RESIDUE NES B 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WYC)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp A:124 -Pro A:125
2Gly A:149 -Lys A:150
3Asp B:124 -Pro B:125
4Gly B:149 -Lys B:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WYC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WYC)

(-) Exons   (0, 0)

(no "Exon" information available for 3WYC)

(-) 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:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhh....eeeeeeee..hhhhh......eeee.hhhhhhh....eeee.....hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhh..eeeeeee..eehhhhhhhhhh...eeeeeeeeeehhhhhhhhhh......hhhhheeeeeeeee....hhhhhhhhhhh.........eeeee.hhhhhhhhh....eeeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wyc A   2 SKIRIGIVGYGNLGRGVEAAIQQNPDMELVAVFTRRDPKTVAVKSNVKVLHVDDAQSYKDEIDVMILCGGSATDLPEQGPYFAQYFNTIDSFDTHARIPDYFDAVNAAAEQSGKVAIISVGWDPGLFSLNRLLGEVVLPVGNTYTFWGKGVSQGHSDAIRRIQGVKNAVQYTIPIDEAVNRVRSGENPELSTREKHARECFVVLEEGADPAKVEHEIKTMPNYFDEYDTTVHFISEEELKQNHSGMPHGGFVIRSGKSDEGHKQIIEFSLNLESNPMFTSSALVAYARAAYRLSQNGDKGAKTVFDIPFGLLSPKSPEDLRKELLTR 328
                                    11        21        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       


Chain B from PDB  Type:PROTEIN  Length:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhh....eeeeeeee..hhhhh......eeee.hhhhhhh....eeee.....hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhh..eeeeeee..eehhhhhhhhhh...eeeeeeeeeehhhhhhhhhh......hhhhheeeeeeeee....hhhhhhhhhhh.........eeeee.hhhhhhhhh....eeeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wyc B   2 SKIRIGIVGYGNLGRGVEAAIQQNPDMELVAVFTRRDPKTVAVKSNVKVLHVDDAQSYKDEIDVMILCGGSATDLPEQGPYFAQYFNTIDSFDTHARIPDYFDAVNAAAEQSGKVAIISVGWDPGLFSLNRLLGEVVLPVGNTYTFWGKGVSQGHSDAIRRIQGVKNAVQYTIPIDEAVNRVRSGENPELSTREKHARECFVVLEEGADPAKVEHEIKTMPNYFDEYDTTVHFISEEELKQNHSGMPHGGFVIRSGKSDEGHKQIIEFSLNLESNPMFTSSALVAYARAAYRLSQNGDKGAKTVFDIPFGLLSPKSPEDLRKELLTR 328
                                    11        21        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
   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 3WYC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WYC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WYC)

(-) Gene Ontology  (8, 8)

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
    NAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NES  [ 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 ]
 
  Cis Peptide Bonds
    Asp A:124 - Pro A:125   [ RasMol ]  
    Asp B:124 - Pro B:125   [ RasMol ]  
    Gly A:149 - Lys A:150   [ RasMol ]  
    Gly B:149 - Lys B:150   [ RasMol ]  
 

(-) 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
  3wyc
    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
  DAPDH_URETH | G1UII1
    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)
  1.4.1.16
    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
  DAPDH_URETH | G1UII1
    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
        DAPDH_URETH | G1UII1: 3wyb 5gz1 5gz3 5gz6

(-) Related Entries Specified in the PDB File

3wyb