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 :  PBP ACCA FROM A. TUMEFACIENS C58 IN COMPLEX WITH AGROCINOPINE A
 
Authors :  A. El Sahili, S. Morera
Date :  20 Apr 15  (Deposition) - 19 Aug 15  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pbp, Class C, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. El Sahili, S. Z. Li, J. Lang, C. Virus, S. Planamente, M. Ahmar, B. G. Guimaraes, M. Aumont-Nicaise, A. Vigouroux, L. Soulere, J. Reader, Y. Queneau, D. Faure, S. Morera
A Pyranose-2-Phosphate Motif Is Responsible For Both Antibiotic Import And Quorum-Sensing Regulation In Agrobacterium Tumefaciens.
Plos Pathog. V. 11 05071 2015
PubMed-ID: 26244338  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1005071

(-) Compounds

Molecule 1 - ABC TRANSPORTER, SUBSTRATE BINDING PROTEIN (AGROCINOPINES A AND B)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 30-521
    Gene: ACCA, ATU6139
    Organism Scientific: AGROBACTERIUM TUMEFACIENS (STRAIN C58 / ATCC 33970)
    Organism Taxid: 176299

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1AGR2Ligand/Ion[(2R,3S,4S,5S)-2,5-BIS(HYDROXYMETHYL)-5-[(2R,3R,4R,5R,6R)-6-(HYDROXYMETHYL)-3,4,5-TRIS(OXIDANYL)OXAN-2-YL]OXY-4-OXIDANYL-OXOLAN-3-YL] [(2R,3R,4S,5S)-2,4,5-TRIS(OXIDANYL)OXAN-3-YL] HYDROGEN PHOSPHATE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1AGR1Ligand/Ion[(2R,3S,4S,5S)-2,5-BIS(HYDROXYMETHYL)-5-[(2R,3R,4R,5R,6R)-6-(HYDROXYMETHYL)-3,4,5-TRIS(OXIDANYL)OXAN-2-YL]OXY-4-OXIDANYL-OXOLAN-3-YL] [(2R,3R,4S,5S)-2,4,5-TRIS(OXIDANYL)OXAN-3-YL] HYDROGEN PHOSPHATE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1AGR1Ligand/Ion[(2R,3S,4S,5S)-2,5-BIS(HYDROXYMETHYL)-5-[(2R,3R,4R,5R,6R)-6-(HYDROXYMETHYL)-3,4,5-TRIS(OXIDANYL)OXAN-2-YL]OXY-4-OXIDANYL-OXOLAN-3-YL] [(2R,3R,4S,5S)-2,4,5-TRIS(OXIDANYL)OXAN-3-YL] HYDROGEN PHOSPHATE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:42 , PRO A:43 , ASN A:44 , SER A:53 , ASN A:54 , VAL A:55 , TYR A:145 , TRP A:178 , ASN A:284 , MET A:372 , TYR A:375 , TYR A:376 , TYR A:402 , GLY A:405 , TRP A:418 , SER A:419 , ASN A:420 , GLY A:421 , GLU A:434 , GLU A:510 , HOH A:714 , HOH A:762 , HOH A:810 , HOH A:894binding site for residue AGR A 601
2AC2SOFTWAREVAL A:154 , ASP A:156 , LYS A:157 , LYS A:199binding site for residue EDO A 602
3AC3SOFTWARELEU B:42 , PRO B:43 , ASN B:44 , ILE B:52 , SER B:53 , ASN B:54 , VAL B:55 , TYR B:145 , TRP B:178 , ASN B:284 , MET B:372 , TYR B:375 , TYR B:376 , TYR B:402 , PRO B:404 , PHE B:407 , TRP B:418 , SER B:419 , ASN B:420 , GLY B:421 , GLU B:434 , GLU B:510 , HOH B:723 , HOH B:854binding site for residue AGR B 601
4AC4SOFTWAREASP B:119 , TYR B:123 , GLU B:128 , LYS B:185binding site for residue PEG B 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala A:429 -Thr A:430
2Gly B:405 -Ser B:406
3Ala B:429 -Thr B:430

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZEB)

(-) 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:490
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee................hhhhhhhhh...eee..hhhhh......eee..eeeeeeee..eeeeee............hhhhhhhhh......hhhhh....hhhhhh..eeeeeeee..eeeeee.....hhhhhhh.......hhhhhhhhhhhhhhhh......eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeeeehhhhhhhhhh...eeeeeee..eeeeeee...hhhhhhhhhhhhhhhh.hhhhhhhhhhh..........hhhhhhhh.........hhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhh....eeeee.......hhhhh.eeeeeee.....hhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeeee..eeeeeee..ee...............ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zeb A  32 RRALRLGVNGLPNSLEPVNAISNVGPRIVNQIFDTLIARDFFAKGAPGNAIDLVPALAESWERIDEKSVRFKLRQKVMFHDGVELTADDVAYTFSSERLWGPEAIKKIPLGKSYSLDFDEPVVEDKYTVTLRTKTPSYLIETFVASWMSRIVPKEYYKKLGAVDFGNKPVGTGPYKFVEFVAGDRVVLEANDAYWGPKPTASKITYQIVAEPATRVAGLISGEYDIITTLTPDDIQLINSYPDLETRGTLIENFHMFTFNMNQEVFKDKKLRRALALAVNRPIMVEALWKKQASIPAGFNFPNYGETFDPKRKAMEYNVEEAKRLVKESGYDGTPITYHTMGNYYANAMPALMMMIEMWKQIGVNVVMKTYAPGSFPPDNQTWMRNWSNGQWMTDAYATIVPEFGPNGQVQKRWGWKAPAEFNELCQKVTVLPNGKERFDAYNRMRDIFEEEAPAVILYQPYDVYAARKDVHWKPVSFEMMEFRNNLSFG 521
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521


Chain B from PDB  Type:PROTEIN  Length:489
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee................hhhhhhhhh...eee..hhhhh......eee..eeeeeeee..eeeeee............hhhhhhhhh......hhhhh....hhhhhh..eeeeeeee..eeeeee.....hhhhhhh.......hhhhhhhhhhhhhhhh......eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh...eeeeehhhhhhhhhh...eeeeeee..eeeeeee...hhhhh.hhhhhhhhhh.hhhhhhhhhhh..........hhhhhhhh.........hhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhh....eeeee.......hhhhh.eeeeeee.....hhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeeee..eeeeeee..ee...............ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zeb B  32 RRALRLGVNGLPNSLEPVNAISNVGPRIVNQIFDTLIARDFFAKGAPGNAIDLVPALAESWERIDEKSVRFKLRQKVMFHDGVELTADDVAYTFSSERLWGPEAIKKIPLGKSYSLDFDEPVVEDKYTVTLRTKTPSYLIETFVASWMSRIVPKEYYKKLGAVDFGNKPVGTGPYKFVEFVAGDRVVLEANDAYWGPKPTASKITYQIVAEPATRVAGLISEYDIITTLTPDDIQLINSYPDLETRGTLIENFHMFTFNMNQEVFKDKKLRRALALAVNRPIMVEALWKKQASIPAGFNFPNYGETFDPKRKAMEYNVEEAKRLVKESGYDGTPITYHTMGNYYANAMPALMMMIEMWKQIGVNVVMKTYAPGSFPPDNQTWMRNWSNGQWMTDAYATIVPEFGPNGQVQKRWGWKAPAEFNELCQKVTVLPNGKERFDAYNRMRDIFEEEAPAVILYQPYDVYAARKDVHWKPVSFEMMEFRNNLSFG 521
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251||     262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512         
                                                                                                                                                                                                                                                      252|                                                                                                                                                                                                                                                                           
                                                                                                                                                                                                                                                       254
   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 4ZEB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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
    AGR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:429 - Thr A:430   [ RasMol ]  
    Ala B:429 - Thr B:430   [ RasMol ]  
    Gly B:405 - Ser B:406   [ 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
  4zeb
    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
  Q7D2F4_AGRFC | Q7D2F4
    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
  Q7D2F4_AGRFC | Q7D2F4
    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
        Q7D2F4_AGRFC | Q7D2F4: 4zei
UniProtKB/TrEMBL
        Q7D2F4_AGRFC | Q7D2F4: 4ra1 4ze8 4ze9 4zec 4zed

(-) Related Entries Specified in the PDB File

4ra1 4ze8 4ze9