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 :  CRYSTAL STRUCTURE OF THE CBS-DOMAIN CONTAINING PROTEIN ATU1752 FROM AGROBACTERIUM TUMEFACIENS
 
Authors :  A. U. Singer, X. Xu, R. Zhang, H. Cui, M. Kudritsdka, A. M. Edwards, A. Joa A. F. Yakunin, A. Savchenko, Midwest Center For Structural Genom (Mcsg)
Date :  09 Dec 08  (Deposition) - 13 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Cbs Domain, Prokaryotic, Bound Nucleotide, Amp, Nadh, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function, Nucleotide-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. U. Singer, G. Brown, M. Proudfoot, X. Xu, A. Dong, H. Cui, A. M. Edwards, A. Joachimiak, A. Savchenko, A. F. Yakunin
Crystal Structure Of The Cbs-Domain Containing Protein Atu1752 From Agrobacterium Tumefaciens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN ATU1752
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TVLIC
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AGR_C_3216, ATU1752
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid: 176299
    Strain: C58

 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  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1AMP4Ligand/IonADENOSINE MONOPHOSPHATE
2NAI4Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3SO42Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:52 , THR A:54 , ARG A:56 , ASP A:57 , THR A:79 , ASN A:81 , VAL A:83 , PHE A:103 , ARG A:104 , HIS A:105 , PRO A:107BINDING SITE FOR RESIDUE AMP A 200
02AC2SOFTWARELYS A:12 , ASP A:15 , VAL A:16 , VAL A:17 , ILE A:37 , GLY A:38 , ALA A:39 , HIS A:105 , ILE A:117 , SER A:119 , GLY A:121 , ASP A:122 , LYS A:125 , ARG D:56 , MET D:98 , THR D:99 , ARG D:102 , PHE D:103 , ARG D:104BINDING SITE FOR RESIDUE NAI A 211
03AC3SOFTWARELYS A:80 , ASN A:81BINDING SITE FOR RESIDUE SO4 A 145
04AC4SOFTWAREILE B:52 , THR B:54 , ASP B:57 , THR B:79 , ASN B:81 , VAL B:83 , PHE B:103 , ARG B:104 , HIS B:105BINDING SITE FOR RESIDUE AMP B 200
05AC5SOFTWARELYS B:12 , ASP B:15 , VAL B:16 , VAL B:17 , ILE B:37 , GLY B:38 , ALA B:39 , HIS B:105 , ILE B:117 , SER B:119 , ILE B:120 , GLY B:121 , ASP B:122 , LYS B:125 , ARG C:56 , MET C:98 , THR C:99 , ARG C:102 , PHE C:103 , ARG C:104BINDING SITE FOR RESIDUE NAI B 211
06AC6SOFTWARETHR B:79 , LYS B:80 , ASN B:81BINDING SITE FOR RESIDUE SO4 B 145
07AC7SOFTWAREILE C:52 , THR C:54 , ASP C:57 , THR C:79 , VAL C:83 , PHE C:103 , ARG C:104 , HIS C:105 , PRO C:107BINDING SITE FOR RESIDUE AMP C 200
08AC8SOFTWAREARG B:56 , MET B:98 , THR B:99 , ARG B:102 , PHE B:103 , ARG B:104 , LYS C:12 , ASP C:15 , VAL C:17 , ILE C:37 , GLY C:38 , ALA C:39 , HIS C:105 , ILE C:117 , SER C:119 , GLY C:121 , ASP C:122 , LYS C:125 , HOH C:152BINDING SITE FOR RESIDUE NAI C 211
09AC9SOFTWARETHR C:79 , LYS C:80 , ASN C:81BINDING SITE FOR RESIDUE SO4 C 145
10BC1SOFTWAREILE D:52 , THR D:54 , ASP D:57 , THR D:79 , ASN D:81 , VAL D:83 , PHE D:103 , ARG D:104 , HIS D:105 , PRO D:107BINDING SITE FOR RESIDUE AMP D 200
11BC2SOFTWAREARG A:56 , MET A:98 , ARG A:102 , PHE A:103 , ARG A:104 , LYS D:12 , ASP D:15 , VAL D:16 , VAL D:17 , ILE D:37 , GLY D:38 , ALA D:39 , HIS D:105 , ILE D:117 , SER D:119 , ILE D:120 , GLY D:121 , ASP D:122 , LYS D:125BINDING SITE FOR RESIDUE NAI D 211
12BC3SOFTWAREMET D:78 , THR D:79 , LYS D:80 , ASN D:81BINDING SITE FOR RESIDUE SO4 D 145

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FHM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FHM)

(-) 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:136
 aligned with A9CIP4_AGRFC | A9CIP4 from UniProtKB/TrEMBL  Length:144

    Alignment length:136
                                  1                                                                                                                                 
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124      
         A9CIP4_AGRFC     - ------MATFVKDLLDRKGRDVVTVGPDVSIGEAAGTLHAHKIGAVVVTDADGVVLGIFTERDLVKAVAGQGAASLQQSVSVAMTKNVVRCQHNSTTDQLMEIMTGGRFRHVPVEENGRLAGIISIGDVVKARIGE 130
               SCOP domains d3fhma_ A: automated matches                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh....ee....hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhhhhhhhhh.hhhhh............hhhhhhhhhhhhh..eeeeee..eeeeeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fhm A  -5 NLYFQGMATFVKDLLDRKGRDVVTVGPDVSIGEAAGTLHAHKIGAVVVTDADGVVLGIFTERDLVKAVAGQGAASLQQSVSVAMTKNVVRCQHNSTTDQLMEIMTGGRFRHVPVEENGRLAGIISIGDVVKARIGE 130
                                     4        14        24        34        44        54        64        74        84        94       104       114       124      


Chain B from PDB  Type:PROTEIN  Length:126
 aligned with A9CIP4_AGRFC | A9CIP4 from UniProtKB/TrEMBL  Length:144

    Alignment length:126
                                    12        22        32        42        52        62        72        82        92       102       112       122      
         A9CIP4_AGRFC     3 TFVKDLLDRKGRDVVTVGPDVSIGEAAGTLHAHKIGAVVVTDADGVVLGIFTERDLVKAVAGQGAASLQQSVSVAMTKNVVRCQHNSTTDQLMEIMTGGRFRHVPVEENGRLAGIISIGDVVKARI 128
               SCOP domains d3fhmb_ B: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh....ee....hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhhhhhhhhh.hhhhh............hhhhhhhhhhhhh..eeeeee..eeeeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fhm B   3 TFVKDLLDRKGRDVVTVGPDVSIGEAAGTLHAHKIGAVVVTDADGVVLGIFTERDLVKAVAGQGAASLQQSVSVAMTKNVVRCQHNSTTDQLMEIMTGGRFRHVPVEENGRLAGIISIGDVVKARI 128
                                    12        22        32        42        52        62        72        82        92       102       112       122      


Chain C from PDB  Type:PROTEIN  Length:134
 aligned with A9CIP4_AGRFC | A9CIP4 from UniProtKB/TrEMBL  Length:144

    Alignment length:134
                                  1                                                                                                                               
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124    
         A9CIP4_AGRFC     - ------MATFVKDLLDRKGRDVVTVGPDVSIGEAAGTLHAHKIGAVVVTDADGVVLGIFTERDLVKAVAGQGAASLQQSVSVAMTKNVVRCQHNSTTDQLMEIMTGGRFRHVPVEENGRLAGIISIGDVVKARI 128
               SCOP domains d3fhmc_ C: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh....ee....hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhhhhhhhhh.hhhhh............hhhhhhhhhhhhh..eeeeee..eeeeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fhm C  -5 NLYFQGMATFVKDLLDRKGRDVVTVGPDVSIGEAAGTLHAHKIGAVVVTDADGVVLGIFTERDLVKAVAGQGAASLQQSVSVAMTKNVVRCQHNSTTDQLMEIMTGGRFRHVPVEENGRLAGIISIGDVVKARI 128
                                     4        14        24        34        44        54        64        74        84        94       104       114       124    


Chain D from PDB  Type:PROTEIN  Length:125
 aligned with A9CIP4_AGRFC | A9CIP4 from UniProtKB/TrEMBL  Length:144

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
         A9CIP4_AGRFC     2 ATFVKDLLDRKGRDVVTVGPDVSIGEAAGTLHAHKIGAVVVTDADGVVLGIFTERDLVKAVAGQGAASLQQSVSVAMTKNVVRCQHNSTTDQLMEIMTGGRFRHVPVEENGRLAGIISIGDVVKARI 128
               SCOP domains d3fhmd_ D: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh....ee....hhhhhhhhhhhh...eeeee.....eeeeeehhhhhhhhhhhhhhhhh.hhhhh............hhhhhhhhhhhhh..eeee.--....eeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fhm D   2 ATFVKDLLDRKGRDVVTVGPDVSIGEAAGTLHAHKIGAVVVTDADGVVLGIFTERDLVKAVAGQGAASLQQSVSVAMTKNVVRCQHNSTTDQLMEIMTGGRFRHVPVE--GRLAGIISIGDVVKARI 128
                                    11        21        31        41        51        61        71        81        91       101       | -|      121       
                                                                                                                                     109  |                
                                                                                                                                        112
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A9CIP4_AGRFC | A9CIP4)
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 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
    AMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAI  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3fhm)
 
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
  3fhm
    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
  A9CIP4_AGRFC | A9CIP4
    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
  A9CIP4_AGRFC | A9CIP4
    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 3FHM)

(-) Related Entries Specified in the PDB File

2rc3 CRYSTAL STRUCTURE OF CBS DOMAIN, NE2398 RELATED ID: APC7156 RELATED DB: TARGETDB