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 :  1.5 ANGSTROM CRYSTAL STRUCTURE OF THE COMPLEX OF LIGAND BINDING COMPONENT OF ABC-TYPE IMPORT SYSTEM FROM STAPHYLOCOCCUS AUREUS WITH NICKEL AND TWO HISTIDINES
 
Authors :  G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, O. Kiry F. Falugi, M. Bottomley, F. Bagnoli, G. Grandi, W. F. Anderson, Center Structural Genomics Of Infectious Diseases (Csgid)
Date :  28 Apr 11  (Deposition) - 11 May 11  (Release) - 11 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligand Binding Component, Abc-Type Import System, Nickel, Single Or Di-Peptides, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, O. Kiryukhina, F. Falugi, M. Bottomley, F. Bagnoli, G. Grandi, W. F. Anderson
1. 5 Angstrom Crystal Structure Of The Complex Of Ligand Binding Component Of Abc-Type Import System From Staphylococcus Aureus With Nickel And Two Histidines.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 15B
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LIGAND BINDING COMPONENT
    Gene: SAOUHSC_00001, SAOUHSC_00201
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 93061
    Strain: NCTC 8325

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2HIS2Mod. Amino AcidHISTIDINE
3MSE6Mod. Amino AcidSELENOMETHIONINE
4NI1Ligand/IonNICKEL (II) ION
5SO44Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:25 , ARG A:231 , GLU A:352 , TYR A:366 , SER A:367 , PHE A:368 , GLY A:369 , ILE A:390 , HIS A:472 , NI A:473 , HOH A:843 , HOH A:915BINDING SITE FOR RESIDUE HIS A 471
2AC2SOFTWARELEU A:14 , ARG A:231 , TYR A:319 , ARG A:322 , ILE A:351 , GLU A:352 , TYR A:366 , SER A:367 , HIS A:471 , NI A:473 , HOH A:811BINDING SITE FOR RESIDUE HIS A 472
3AC3SOFTWAREHIS A:471 , HIS A:472BINDING SITE FOR RESIDUE NI A 473
4AC4SOFTWAREILE A:45 , GLU A:46 , LYS A:47 , TYR A:53 , TYR A:98 , LYS A:386 , ASP A:387 , ASP A:401 , HOH A:765 , HOH A:812 , HOH A:907 , HOH A:1034BINDING SITE FOR RESIDUE EPE A 474
5AC5SOFTWAREGLU A:87 , ILE A:102 , SER A:103 , PRO A:282 , TYR A:283 , HOH A:582 , HOH A:609 , HOH A:674 , HOH A:982BINDING SITE FOR RESIDUE EPE A 475
6AC6SOFTWARELYS A:51 , LYS A:66 , ASP A:67 , ASN A:399 , HOH A:1038BINDING SITE FOR RESIDUE SO4 A 476
7AC7SOFTWAREILE A:216 , GLU A:217 , LEU A:222 , LYS A:223 , VAL A:224 , HOH A:607 , HOH A:668BINDING SITE FOR RESIDUE SO4 A 477
8AC8SOFTWAREGLN A:145 , TYR A:158 , LYS A:159 , GLN A:160 , ARG A:162 , GLN A:330 , GLN A:333 , HOH A:942BINDING SITE FOR RESIDUE SO4 A 478
9AC9SOFTWARELYS A:156 , LYS A:315 , LYS A:346 , TYR A:354 , HOH A:745 , HOH A:1067 , HOH A:1182BINDING SITE FOR RESIDUE SO4 A 479

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RQT)

(-) 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:467
 aligned with Q2G2P5_STAA8 | Q2G2P5 from UniProtKB/TrEMBL  Length:470

    Alignment length:468
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           470  
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464     |  
         Q2G2P5_STAA8     5 GKDLNISLPLKTKSIAPYETDVPVKIGAAESLFKTNDQGKIEKALVKSYHQPNDTTLDIELKDNIKFQNGQKLTAEKVKSSLENSMKKSDLVKYSLPISSITAKGQKLTIKTNSAYPELVSELANPFMAIYDTDAKSDVNQTPVGTGPYQIKDYKQSRKISLSNFKDYWQGKPKLDHITVTYQEDGNNRVRNLESQKDDLITDVPVNKVQDIENNQNLKVSKESGFRTSLLMYNHTNKKMTKSVREALDHIIDRQGIADHIYQGYAKPATSPFNDKIPYIKEPKLTKQNIEQAKMLLAKDGYTKEHPLKIKLITYDGRPELSKIAQVLQSDAKKANIEIDIKSVDDIEGYLKDRSAWDATMYSFGTIPRGDTGYFFNQAYKKDGAINKGDYNNSNVDDLINQLNHTVDVKERHNISNDIIKLSSRDVPNSYIAYNDQIVAANSKVKNYKVTPEGIYLIDYRTTIER--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------------------------SBP_bac_5-3rqtA01 A:44-392                                                                                                                                                                                                                                                                                                                                   -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee............hhhhhh......eee.....eee..eeeeeeee..eeeeee............hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeee.....hhhhhhhhhhhh...................eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eee..hhhhhhhhhhh..eeeeeeeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhh....eee....................hhhhhhhhhhh........eeeeeee....hhhhhhhhhhhhhhhh..eeeeeee..hhhhhh.......eeeeeee......hhhhhhhhh............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeee..ee................ee.-.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rqt A   5 GKDLNISLPLKTKSIAPYETDVPVKIGAAESLFKTNDQGKIEKALVKSYHQPNDTTLDIELKDNIKFQNGQKLTAEKVKSSLENSmKKSDLVKYSLPISSITAKGQKLTIKTNSAYPELVSELANPFmAIYDTDAKSDVNQTPVGTGPYQIKDYKQSRKISLSNFKDYWQGKPKLDHITVTYQEDGNNRVRNLESQKDDLITDVPVNKVQDIENNQNLKVSKESGFRTSLLmYNHTNKKmTKSVREALDHIIDRQGIADHIYQGYAKPATSPFNDKIPYIKEPKLTKQNIEQAKmLLAKDGYTKEHPLKIKLITYDGRPELSKIAQVLQSDAKKANIEIDIKSVDDIEGYLKDRSAWDATmYSFGTIPRGDTGYFFNQAYKKDGAINKGDYNNSNVDDLINQLNHTVDVKERHNISNDIIKLSSRDVPNSYIAYNDQIVAANSKVKNYKVTPEGIYLIDYRTTIE-HH 472
                                    14        24        34        44        54        64        74        84     |  94       104       114       124       134       144       154       164       174       184       194       204       214       224       234 |     244       254       264       274       284       294    |  304       314       324       334       344       354       364|      374       384       394       404       414       424       434       444       454       464    | | 
                                                                                                                90-MSE                                   132-MSE                                                                                                 236-MSE 244-MSE                                                299-MSE                                                           365-MSE                                                                                                 469 | 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            471
   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 3RQT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q2G2P5_STAA8 | Q2G2P5)
molecular function
    GO:0015197    peptide transporter activity    Enables the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells.
biological process
    GO:0015833    peptide transport    The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
cellular component
    GO:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

 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
    EPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HIS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3rqt)
 

(-) 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
  3rqt
    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
  Q2G2P5_STAA8 | Q2G2P5
    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
  Q2G2P5_STAA8 | Q2G2P5
    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 3RQT)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3RQT)