Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)

(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF PROTEIN Q8U9W0 FROM AGROBACTERIUM TUMEFACIENS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ATR55.
 
Authors :  A. P. Kuzin, Y. Chen, F. Forouhar, S. M. Vorobiev, R. Xiao, L. -C. Ma, T. Ac G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomic Consortium (Nesg)
Date :  11 May 05  (Deposition) - 24 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  E (1x),F (1x)
Biol. Unit 4:  D (1x),G (1x)
Biol. Unit 5:  G  (2x)
Keywords :  Nesg, Atr55, Q8U9W0, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Kuzin, Y. Chen, F. Forouhar, S. M. Vorobiev, R. Xiao, L. -C. Ma, T. Acton, G. T. Montelione, J. F. Hunt, L. Tong
X-Ray Structure Of The Hypothetical Protein Q8U9W0 From Agrobacterium Tumefaciens. Northeast Structural Genomics Consortium Target Atr55.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN ATU3615
    Chains: A, B, C, D, E, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3) + MAGIC
    Expression System Taxid: 562
    Expression System Vector: PET21
    Expression System Vector Type: PLASMID
    Gene: AGR L 2421
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR. C58
    Organism Taxid: 176299
    Strain: C58 / ATCC 33970

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFG
Biological Unit 1 (1x): AB     
Biological Unit 2 (1x):  BC    
Biological Unit 3 (1x):     E (1x)F (1x) 
Biological Unit 4 (1x):    D (1x)  G (1x)
Biological Unit 5 (2x):       G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1ZNP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser C:125 -Pro C:126
2Ser C:141 -Pro C:142
3Ser E:125 -Pro E:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZNP)

(-) 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:140
 aligned with A9CFG3_AGRFC | A9CFG3 from UniProtKB/TrEMBL  Length:142

    Alignment length:140
                             1                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139
         A9CFG3_AGRFC     - -MSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVMAEPGWSPG 139
               SCOP domains d1znpa1 A:4-143 Hypothetical protein Atu3615                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.ee.....eeeeeee..........eeeeeeee....eeeeee....eeeeeeee..eeeeee......eeeee.......ee.eeee....eeeeee...eeeeeeee....hhh.eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1znp A   4 DmSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVmAEPGWSPG 143
                             |      13        23        33        43        53        63        73        83        93       103       113       123       133 |     143
                             |                                                                                                                               135-MSE    
                             5-MSE                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with A9CFG3_AGRFC | A9CFG3 from UniProtKB/TrEMBL  Length:142

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
         A9CFG3_AGRFC     1 MSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVMAEPGWSPGD 140
               SCOP domains d1znpb_ B: Hypothetical protein Atu3615                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.ee.....eeeeeee..........eeeeeeee....eeeeee....eeeeeeee..eeeeee......eeeee..........eeee....eeeeee...eeeeeeee....hhh.eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1znp B   5 mSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVmAEPGWSPGD 144
                            |       14        24        34        44        54        64        74        84        94       104       114       124       134|      144
                            5-MSE                                                                                                                           135-MSE     


Chain C from PDB  Type:PROTEIN  Length:138
 aligned with A9CFG3_AGRFC | A9CFG3 from UniProtKB/TrEMBL  Length:142

    Alignment length:138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        
         A9CFG3_AGRFC     1 MSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVMAEPGWSP 138
               SCOP domains d1znpc_ C: Hypothetical protein Atu3615                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhh..ee.....eeeeeee..........eeeeeeee.......eee...eeeeeeeee..eeeeee......eeeee..hhhhh...eeee....eeeeee...eeeeeeeee...hhh.eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1znp C   5 mSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVmAEPGWSP 142
                            |       14        24        34        44        54        64        74        84        94       104       114       124       134|       
                            5-MSE                                                                                                                           135-MSE   


Chain D from PDB  Type:PROTEIN  Length:138
 aligned with A9CFG3_AGRFC | A9CFG3 from UniProtKB/TrEMBL  Length:142

    Alignment length:138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        
         A9CFG3_AGRFC     1 MSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVMAEPGWSP 138
               SCOP domains d1znpd_ D: Hypothetical protein Atu3615                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh.ee.....eeeeeee..........eeeeeeee.......eee....eeeeeeee..eeeeee......eeeee..hhhhh...eeee....eeeeee...eeeeeeee....hhh.eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1znp D   5 mSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVmAEPGWSP 142
                            |       14        24        34        44        54        64        74        84        94       104       114       124       134|       
                            5-MSE                                                                                                                           135-MSE   


Chain E from PDB  Type:PROTEIN  Length:139
 aligned with A9CFG3_AGRFC | A9CFG3 from UniProtKB/TrEMBL  Length:142

    Alignment length:139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         
         A9CFG3_AGRFC     1 MSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVMAEPGWSPG 139
               SCOP domains d1znpe_ E: Hypothetical protein Atu3615                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.ee.....eeeeeee..........eeeeeeee.......eee...eeeeeeeee..eeeeee......eeeee..hhhhh...eeee....eeeeee...eeeeeeeee...hhh.eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1znp E   5 mSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVmAEPGWSPG 143
                            |       14        24        34        44        54        64        74        84        94       104       114       124       134|        
                            5-MSE                                                                                                                           135-MSE    


Chain F from PDB  Type:PROTEIN  Length:140
 aligned with A9CFG3_AGRFC | A9CFG3 from UniProtKB/TrEMBL  Length:142

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
         A9CFG3_AGRFC     1 MSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVMAEPGWSPGD 140
               SCOP domains d1znpf_ F: Hypothetical protein Atu3615                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.ee.....eeeeeee..........eeeeeeee.......eee....eeeeeeee..eeeeee......eeeee..........eeee....eeeeee...eeeeeeee....hhh.eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1znp F   5 mSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVmAEPGWSPGD 144
                            |       14        24        34        44        54        64        74        84        94       104       114       124       134|      144
                            5-MSE                                                                                                                           135-MSE     


Chain G from PDB  Type:PROTEIN  Length:140
 aligned with A9CFG3_AGRFC | A9CFG3 from UniProtKB/TrEMBL  Length:142

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
         A9CFG3_AGRFC     1 MSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVMAEPGWSPGD 140
               SCOP domains d1znpg_ G: Hypothetical protein Atu3615                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.ee.....eeeeeee..........eeeeeeee....eeeeee....eeeeeeee..eeeeee......eeeee..........eeee....eeeeee...eeeeeeee....hhh.eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1znp G   5 mSAQAIIRELGLEPHPEGGFYHQTFRDKAGGERGHSTAIYYLLEKGVRSHWHRVTDAVEVWHYYAGAPIALHLSQDGREVQTFTLGPAILEGERPQVIVPANCWQSAESLGDFTLVGCTVSPGFAFSSFVmAEPGWSPGD 144
                            |       14        24        34        44        54        64        74        84        94       104       114       124       134|      144
                            5-MSE                                                                                                                           135-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, 7)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZNP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ZNP)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1ZNP)

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1znp)
 
  Cis Peptide Bonds
    Ser C:125 - Pro C:126   [ RasMol ]  
    Ser C:141 - Pro C:142   [ RasMol ]  
    Ser E:125 - Pro E:126   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format | Biol. Unit 5 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
  1znp
    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
  A9CFG3_AGRFC | A9CFG3
    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
  A9CFG3_AGRFC | A9CFG3
    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 1ZNP)

(-) Related Entries Specified in the PDB File

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